diff --git a/.gitignore b/.gitignore index d1b7468..00d2c60 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,14 @@ __pycache__ artistlib.egg-info -dist \ No newline at end of file +dist +/venv/ +/.venv/ +*.tif +/workspace/ +*.raw +*.stl +*.json +*.aRTist +*.ply +/build/ +/examples/ \ No newline at end of file diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..c8cfe39 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.10 diff --git a/SimulateFromList/ListOfSimulations.txt b/SimulateFromList/ListOfSimulations.txt deleted file mode 100644 index 2160ad3..0000000 --- a/SimulateFromList/ListOfSimulations.txt +++ /dev/null @@ -1,449 +0,0 @@ -ID LG LG Thickness Spot size Spot resolution Sampling ETA Source Type Source U Source I Source Filter Material Source Filter Thickness N Detector pixel size Cone beam angle Other parameters Filename Remarks -1 6 2 0.002 301 1089 0 Mono 50 1 VOID 0 10 0.1 0.05 NxS_UB_ConeBeamAngle.tif -2 6 2 0.002 301 1089 0 Mono 50 1 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1089 0 Mono 50 1 VOID 0 10 0.1 9.2 NxS_UB_ConeBeamAngle.tif -445 6 16 0.002 301 1089 0 Mono 50 1 VOID 0 10 0.1 9.4 NxS_UB_ConeBeamAngle.tif -446 6 16 0.002 301 1089 0 Mono 50 1 VOID 0 10 0.1 9.6 NxS_UB_ConeBeamAngle.tif -447 6 16 0.002 301 1089 0 Mono 50 1 VOID 0 10 0.1 9.8 NxS_UB_ConeBeamAngle.tif -448 6 16 0.002 301 1089 0 Mono 50 1 VOID 0 10 0.1 10 NxS_UB_ConeBeamAngle.tif diff --git a/SimulateFromList/SimulateFromList.py b/SimulateFromList/SimulateFromList.py deleted file mode 100644 index addd95e..0000000 --- a/SimulateFromList/SimulateFromList.py +++ /dev/null @@ -1,146 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Created on Tue May 31 11:04:16 2022 - -@author: dschumac - -The aRTist.py library needs to be present! -This is an example scipt which shows how to use a spreadsheet to simulate a bunch of images. The corresponding spreadsheet for this script is as a tab-separeted text-file ("ListOfSimulations.txt"). -Each row in the spreadsheet corresponds to a single aRTist simulation. The colums represent the individual simulation parameters. -The given comlumns need to be adapted according to the simulation task, as the script needs to be! - -""" - -import pandas as pd -import os -import sys -sys.path.insert(1, '[Your python library directory]/aRTist-PythonLib') -import aRTist -import math - - - - -######################## Options ############################### -''' aRTist connection ''' -HOST = "127.0.0.1" # localhost -PORT = 3658 # port @HOST -buffer = 1024 # package size -timeout = 10 # TimeOut in sec - - - -''' Path ''' -#Cone Beam -path_script = "[Your directory]/ListOfSimulations.txt" -path_save_images = "[Your directory]/Images_UB_ConeBeam/" - - - - -############################################################################## -''' Read Script file''' - -data = pd.read_csv(path_script, sep="\t", encoding='mbcs') #Read data -data.dropna(axis=0, how='all', inplace=True) #Delete empty rows -data["Filename"].fillna('NA', inplace = True) #Replace empty file names with "NA" -data_sort = data.sort_values(by=['ETA', 'ID']) #sort by ID and spot size - - -############################################################################### -''' Connect to aRTist ''' -Con = aRTist.Connection(HOST, PORT, buffer, timeout) - -############################################################################### -aRTist.Connection.send(Con, aRTist.SETUP_Preview(1)) - -"""Source Setup""" -SourceZ = 10 #Random SZ pos, outside of object -SourcekV = data_sort['Source U'].iloc[0] -SourcemA = data_sort['Source I'].iloc[0] -SourceType = data_sort['Source Type'].iloc[0] -SourceFilterMat = data_sort['Source Filter Material'].iloc[0] -SourceFilterTh = data_sort['Source Filter Thickness'].iloc[0] -sampling = data_sort['Sampling'].iloc[0] - -aRTist.Connection.send(Con, aRTist.SETUP_source(SourceZ, SourcekV, SourcemA, SourceType, SourceFilterMat, SourceFilterTh)) -aRTist.Connection.send(Con, aRTist.SETUP_SourceSampling(sampling)) - - -eta_out = -1 # for checking if ETA has changed -FS_out = -1 # for checking if FS has changed - -for index, row in data_sort.iterrows(): - - Fname = data_sort.loc[index, 'Filename'] - Fname = os.path.splitext(Fname)[0] #extract name without extension - - """Detector position and pixel size""" - PixelSize = data_sort.loc[index, 'Detector pixel size'] - - - """Spot Setup""" - FS = data_sort.loc[index, 'Spot size'] - eta = data_sort.loc[index, 'ETA'] - SpotRes = data_sort.loc[index, 'Spot resolution'] - - """Scene Setup""" - LG = data_sort.loc[index, 'LG'] - name = 'LG{:.0f}'.format(LG) # create object name similar to list in aRTist - Obj = aRTist.Connection.send(Con, aRTist.get_ObjID(name)).split() # Query Object ID from name - OID = Obj[1] # isolate Object ID - aRTist.Connection.send(Con, aRTist.set_vis_AllParts("off")) # set visibility of all objects off - aRTist.Connection.send(Con, aRTist.set_vis(OID, 'on')) # activate object with only - - """Calc magnification, source and detector Z pos""" - cba = data_sort.loc[index, 'Cone beam angle'] # Read cone beam angle - CBA = cba*math.pi/180 # Degree to radian - - GW = LG*9 # group width for 5 lines and 4 gaps in um!! - N = data_sort.loc[index, 'N'] # No. of pixels representing unsharpness - Mag = N*PixelSize/FS+1 # Magnification - SZ = (GW/1000) / (2 * math.sin(CBA)) # Source Z position (SOD) - DetZ = -SZ * (Mag-1) # Detector Z position (SOD) - aRTist.Connection.send(Con, aRTist.set_position('S', 0, 0, SZ)) - - '''Set object thickness (and other dimensions)''' - sizeX = GW*10/3000 - sizeY = GW/1000 - sizeZ = data_sort.loc[index, 'LG Thickness']/1000 - aRTist.Connection.send(Con, aRTist.resize(OID, sizeX, sizeY, sizeZ)) - - - """Calc Detector Size""" - ePS = PixelSize*1000 / Mag # effective pixel size - DetSizeX = int(GW / ePS * 1.5) # Detector length 1.5x group width to limit calc and analysis time - DetSizeY = int(GW / ePS * 2.5) # Detector widht 2.5x group width to allow for background fitting - aRTist.Connection.send(Con, aRTist.SETUP_detector(DetZ, 0, DetSizeX, DetSizeY, PixelSize, 'max', 50000)) - - - if eta != eta_out or FS != FS_out: # Only calc new source when ETA or FS have changed - aRTist.Connection.send(Con, aRTist.SETUP_CalcFocalspot(FS, FS, eta, SpotRes)) - - - aRTist.Connection.send(Con, aRTist.Clear_FF()) - aRTist.Connection.send(Con, aRTist.AutoAcq_FF(1)) - eta_out = eta - FS_out = FS - - aRTist.Connection.send(Con, aRTist.RenderPreview()) - - - #Print name to update user - # print('ID={}, ETA={:.1f}; LG={:.0f} um; Spot={:.1f} um; Sampling={:.0f}; N={:.1f}; {}'.format(index, eta, LG, FS*1000, sampling, N, Fname)) - print('ID={}, CB={:.2f}°; ETA={:.1f}; LG={:.0f} um; Thickness {:.0f} um; Spot={:.1f} um; Sampling={}; N={:.1f}; {}'.format(index, cba, eta, LG, sizeZ*1000, FS*1000, sampling, N, Fname)) - ResFname = '{}_CB{:.2f}_ETA{:.1f}_LG{:.0f}_Th{:.0f}_FS{:.1f}um_Sampling{}_N{:.1f}.tif'.format(Fname, cba, eta, LG, sizeZ*1000, FS*1000, sampling, N) - ResPath = path_save_images + ResFname - - - aRTist.Connection.send(Con, aRTist.make_image()) - aRTist.Connection.send(Con, aRTist.save_image(ResPath)) - - - -############################################################################### -''' Close Connection to aRTist''' -Con.S.close() diff --git a/Standalones/ParticlesAndPores/CreateParticlePoreMatrix.py b/Standalones/ParticlesAndPores/CreateParticlePoreMatrix.py deleted file mode 100644 index 6e5d4db..0000000 --- a/Standalones/ParticlesAndPores/CreateParticlePoreMatrix.py +++ /dev/null @@ -1,316 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Created on Fri Oct 30 16:20:50 2020 - -@author: David Schumacher -""" -import socket -import numpy as np -import csv - -########################### Options #################################### -''' aRTist connection ''' -HOST = "127.0.0.1" # localhost -PORT = 3658 # port @HOST -BUFFER_SIZE = 1024 # package size -timeout = 10 # TimeOut in sec - -''' aRTist setup ''' -SolidModNo = 16 # Number of module "Solid" in aRTist (Modules/XX. Solid) - -''' Particles/Pores ''' -D_max = 100 # max particle diameter in micrometer -P_max = 30 # max pore diameter in micrometer -P_min = 5 # min pore diameter in micrometer - -N_ParX = 2 # No. of particles in X-direction -N_ParY = 2 # No. of particles in X-direction - -Mat_par = "{Fe}" # Material of Particle -Mat_pore = "{VOID}" # Material of Pore - - -MAG = 50 # magnification -SDD = 400 # source-detector distance in mm -pitch = 0.1 # ative pixel size (pitch) of the detector in mm -DBorder = 1.5 # detector border (1/2), Factor (particle size) - -DetX = 500 # Detector resolution X -DetY = 500 # Detector resolution Y - -kV = 150 # Voltage of X-ray source -mA = 100 # Current of X-ray source - -''' Paths ''' -path_aRTist_scene = "I:/Simulations/TMP/Pores/Pore_Matrix_Scene.aRTist" -path_save = "I:/Simulations/TMP/Pores/Coordinates_" - - - -error = 0 - -########################### aRTist functions (to be replaced by library!) ################################# -''' Communication with aRTist ''' -def aRTist_connect(): - S = socket.socket() # Create socket (for TCP) - S.connect((HOST, PORT)) # Connect to aRTist - S.settimeout(timeout) - return S - -def aRTist_sent(x): - total = "" - for i in range(len(x)): - # print(i+1, "of", len(x), " commands send") - # print(x[i]) - S.send(x[i].encode()) - total = total + aRTist_listen(1) - return total - -def aRTist_listen(command_no): - total = "" - stop = False - if (command_no == 0): - S.settimeout(0.2) - while (not stop):# and ("SUCCESS" not in total) and ("ERROR" not in total): # as long as server doesn't respond and doesn't contain "SUCCESS" - try: - msg = S.recv(BUFFER_SIZE).decode() # - except socket.timeout as e: - err = e.args[0] - if err == "timed out": - print("Timeout\n") - stop = True - continue - else: - if ("SUCCESS" in msg): - total = total + msg - # print(msg) - stop = True - continue - elif ("ERROR" in msg): - total = total + msg - # print(msg) - stop = True - global error - error = error + 1 - continue - else: - # print(msg) - if (command_no == 0): - print(msg) - total = total + msg - S.settimeout(timeout) - return total - -''' aRTist specific commands ''' -def aRTist_setup(Path): - STR = ["""FileIO::OpenAny """+ Path +"""; -"""] - return STR - -def aRTist_SETUP_detector(x, y, px): - STR = ["""set ::Xdetector(Type) {flat panel}; -""","""set ::Xsetup_private(DGauto) {Size}; -""","""set ::Xsetup(DetectorPixelX) """+ str((int(x))) +"""; -""","""set ::Xsetup(DetectorPixelY) """+ str((int(y))) +"""; -""","""set ::Xsetup_private(DGdx) """+ str(px) +"""; -""","""set ::Xsetup_private(DGdy) """+ str(px) +"""; -""","""set ::Xdetector(AutoD) {max}; -""","""set ::Xdetector(RefGV) 50000; -""","""::XDetector::UpdateGeometry 1; -"""] - return STR - -def aRTist_SETUP_source(pos, kV, mA): - STR = ["""set ::Xsetup(SourceSampling) {point}; -""","""set ::Xsource(Exposure) """+ str(mA) +"""; -""","""set ::Xsource(Tube) {Mono}; -""","""set ::Xsource(Voltage) """+ str(kV) +"""; -""","""::PartList::Invoke S SetPosition 0 0 """+ str(pos) +"""; -""","""::PartList::Invoke S SetRefPos 0 0 """+ str(pos) +"""; -""","""set ::Xdetector(FFCorrRun) 0; -""","""XDetector::FFCorrClearCmd; -""","""::XSource::spectrumOK; -"""] # set ::Engine::RenderPreview 0; - return STR - -def aRTist_SETUP_FFcorr(): - STR = ["""::XDetector::FFCorrGenCmd; -"""] - return STR - -def aRTist_create_sphere(R): - R = 2 * R - STR = ["""::Modules::Run Solid; -""","""set ::Modules::Module""" +str(SolidModNo)+"""::Solid(Type) {ellipsoid}; -""","""set ::Modules::Module""" +str(SolidModNo)+"""::Solid(Equilateral) 1; -""","""set ::Modules::Module""" +str(SolidModNo)+"""::Solid(X) """+ str(R) +"""; -""","""set ::Modules::Module""" +str(SolidModNo)+"""::Solid(PhiResolution) 80; -""","""set ::Modules::Module""" +str(SolidModNo)+"""::Solid(ThetaResolution) 80; -""","""set ::Modules::Module""" +str(SolidModNo)+"""::Solid(GridEllipsoid) 1; -""","""set ::Modules::Module""" +str(SolidModNo)+"""::Solid(VolumeCorrect) 1; -""","""::Modules::Module""" +str(SolidModNo)+"""::GenerateCmd; -"""] - return STR - -def aRTist_set_material(ID, mat): - STR = ["""::PartList::Set """+ str(ID) +""" Material """+ mat +"""; -"""] - return STR - -def aRTist_set_position(ID, x, y, z): - STR = ["""::PartList::Invoke """+ str(ID) +""" SetPosition """+ str(x) +""" """+ str(y) +""" """+ str(z) +"""; -""","""::PartList::Invoke """+ str(ID) +""" SetRefPos """+ str(x) +""" """+ str(y) +""" """+ str(z) +"""; -"""] - return STR - -def aRTist_translate(ID, x, y, z): - STR = ["""::PartList::Invoke """+ str(ID) +""" Translate world """+ str(x) +""" """+ str(y) +""" """+ str(z) +"""; -"""] - return STR - - -def aRTist_vis_off(): - STR = ["""::PartList::Set parts Visible off; -"""] - return STR - -def aRTist_vis_on(ID): - STR = ["""::PartList::Set """+str(ID)+""" Visible on; -"""] - return STR - -def aRTist_resize(ID, size): - STR = ["""::PartList::Invoke """+str(ID)+""" SetSize """+str(size)+""" """+str(size)+""" """+str(size)+"""; -"""] - return STR - -def aRTist_make_image(): - STR = ["""::Engine::StartStopCmd; -"""] - return STR - -def aRTist_save_image(Path): - STR = ["""::Modules::Execute ImageViewer Save16bit """+ Path +""" 1; -"""] - return STR - - - -########################## Conversions ################################ -''' Particle/Pore ''' - -R_max = D_max / 2 / 1000 # max. particle radius in mm -r_max = P_max / 2 / 1000 # max. pore radius in mm -r_min = P_min / 2 / 1000 # min. pore radius in mm - -''' Detector/Source ''' -OZ = SDD / MAG # position of object (in Z-direction) -OZ = SDD - OZ -VX = pitch / MAG # voxel size , i.e. eff. pixel size -DETxy = (DBorder * D_max) / VX / 1000 # detector size (square) in pixel - -P_xy = (DETxy / 2) * VX * 0.9 # origin of particle range[x][y] with 10% border - -############################################################################### - -P_count = N_ParX*N_ParY #No. of Particles/Pores - - -############################################################################### -''' Connect to aRTist ''' -S = aRTist_connect() - -aRTist_listen(0) - -############################################################################### -''' SETUP aRTist scene ''' -print("SETUP aRTist scene") -aRTist_sent(aRTist_setup(path_aRTist_scene)) -print("SETUP Detector aRTist-Scene") -aRTist_sent(aRTist_SETUP_detector(DetX, DetY, pitch)) -print("SETUP Source aRTist-Scene") -aRTist_sent(aRTist_SETUP_source(SDD, kV, mA)) -print("SETUP FFcorr aRTist-Scene") -aRTist_sent(aRTist_SETUP_FFcorr()) -aRTist_sent(["""set ::Xdetector(FFCorrRun) 1; -"""]) #to check!! -print("SETUP FINISH aRTist-Scene") - -############################################################################### -'''Calc Particle/Pore positions:''' -P_ID, P_RAD, P_XYZ, p_RAD, p_ID = [],[],[],[],[] # List of all particles/pores - -n = 0 #loop count -for i in range(N_ParY): - for ii in range(N_ParX): - n += 1 #increment n by 1 - if (i % 2): #ii is odd - X = 2*R_max*ii + R_max - else: #ii is even (incl. 0) - X = 2*R_max*ii # particle position x - - Y = np.sqrt(3*R_max**2)*i # particle position x - - P_XYZ.append([X, Y, OZ]) - P_ID.append(2*n-1) # Particle-ID - p_ID.append(2*n) # Pore-ID - P_RAD.append(R_max) - -print(P_ID) -print(p_ID) -print(P_XYZ) - -############################################################################## -'''Calc Pore distribution:''' -p_RAD = list(np.linspace(r_min, r_max, num=P_count)) #list of pore radii - -############################################################################## -''' Create particles and pores in aRTist ''' -n = -1 #loop count -for i in range(N_ParY): - for ii in range(N_ParX): - n += 1 #increment n by 1 - # Particle - print("Create Particle ", n+1 , "of", P_count) - aRTist_sent(aRTist_create_sphere(R_max)) - aRTist_sent(aRTist_set_material(P_ID[n], Mat_par)) - aRTist_sent(aRTist_set_position(P_ID[n], P_XYZ[n][0], P_XYZ[n][1], P_XYZ[n][2])) - - - # Pore - aRTist_sent(aRTist_create_sphere(p_RAD[n])) - aRTist_sent(aRTist_set_material(p_ID[n], Mat_pore)) - aRTist_sent(aRTist_set_position(p_ID[n], P_XYZ[n][0], P_XYZ[n][1], P_XYZ[n][2])) - - if (i == range(N_ParY)[-1]): - aRTist_sent(["""::Modules::Module""" +str(SolidModNo)+"""::Close; - """]) - -############################################################################## -'Center middle particle at [0,0,z]' - -Shift = [] -for i in range(len(P_XYZ[0])): - diff = (P_XYZ[0][i] - P_XYZ[-1][i]) / 2 - Shift.append(diff) - -aRTist_sent(aRTist_translate('Parts', Shift[0], Shift[1] , Shift[2])) - - - -####################### Save coordinates in CSV #################################### -header = ["Particle ID", "Particle Diameter", "Pore ID", "Pore Diameter", "X", "Y", "Z"] - -with open(path_save +"data.csv", "w", newline ='') as file: - write = csv.writer(file) - write.writerow(header) - - for i in range(P_count): - row = [str(P_ID[i]), str(2*P_RAD[i]), str(p_ID[i]), str(2*p_RAD[i]), str(P_XYZ[i][0]), str(P_XYZ[i][1]), str(P_XYZ[i][2])] - write.writerow(row) - - -############################################################################### -''' Close Connection to aRTist''' -S.close() - \ No newline at end of file diff --git a/Standalones/ParticlesAndPores/Create_SingleParticle+Pores.py b/Standalones/ParticlesAndPores/Create_SingleParticle+Pores.py deleted file mode 100644 index e3e7f50..0000000 --- a/Standalones/ParticlesAndPores/Create_SingleParticle+Pores.py +++ /dev/null @@ -1,328 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Created on Tue Aug 13 19:30:16 2019 -Creates and transates particles/pores -ONLY for 0 to 1 pore, faster and less expensive than creating new objects each time. -@authors: Alexander Funk, David Schumacher -""" - -import socket -import random -import numpy as np -import math -from time import sleep - -############################### Options ####################################### -''' Connection ''' -HOST = "127.0.0.1" # localhost -PORT = 3658 # port @HOST -BUFFER_SIZE = 1024 # package size -timeout = 10 # TimeOut in sec - -''' aRTist Module ''' -SolidModNo = 17 # Number of module "Solid" in aRTist (Modules/XX. Solid) - -''' Particles/Pores ''' -D_max = 100 # max particle diameter in micrometer -D_min = 90 # min particle diameter in micrometer -P_max = 45 # max pore diameter in micrometer -P_min = 10 # min pore diameter in micrometer -N_Par = 10 # No. of particles to be created -pores_max = 5 # max. no. of pores per particle -pores_min = 1 # min. no. of pores per particle -space = 5 / 1000 # space to particle boundary - -''' X-Ray Setup ''' -MAG = 200 # magnification -SDD = 400 # source-detector distance in mm -pitch = 0.1 # native pixel size (pitch) of the detector in mm -DBorder = 1.5 # detector border (1/2), Factor (particle size) - -kV = 15 # Voltage of X-ray source -mA = 100 # Current of X-ray source - -''' Paths ''' -path_aRTist_scene = "I:/Simulations/TMP/Pores/Single_Pore_Scene.aRTist" -path_save_images = "I:/Simulations/TMP/Pores/img_" - - -error = 0 - -############### aRTist functions (to be replaced by library!) ################# -''' Communication with aRTist ''' -def aRTist_connect(): - S = socket.socket() # Create socket (for TCP) - S.connect((HOST, PORT)) # Connect to aRTist - S.settimeout(timeout) - return S - -def aRTist_sent(x): - total = "" - for i in range(len(x)): - # print(i+1, "of", len(x), " commands send") - # print(x[i]) - S.send(x[i].encode()) - total = total + aRTist_listen(1) - return total - -def aRTist_listen(command_no): - total = "" - stop = False - if (command_no == 0): - S.settimeout(0.2) - while (not stop):# and ("SUCCESS" not in total) and ("ERROR" not in total): # as long as server doesn't respond and doesn't contain "SUCCESS" - try: - msg = S.recv(BUFFER_SIZE).decode() # - except socket.timeout as e: - err = e.args[0] - if err == "timed out": - print("Timeout\n") - stop = True - continue - else: - if ("SUCCESS" in msg): - total = total + msg - # print(msg) - stop = True - continue - elif ("ERROR" in msg): - total = total + msg - # print(msg) - stop = True - global error - error = error + 1 - continue - else: - # print(msg) - if (command_no == 0): - print(msg) - total = total + msg - S.settimeout(timeout) - return total - -''' aRTist specific commands ''' -def aRTist_setup(Path): - STR = ["""FileIO::OpenAny """+ Path +"""; -"""] - return STR - -def aRTist_SETUP_detector(x, y, px): - STR = ["""set ::Xdetector(Type) {flat panel}; -""","""set ::Xsetup_private(DGauto) {Size}; -""","""set ::Xsetup(DetectorPixelX) """+ str((int(x))) +"""; -""","""set ::Xsetup(DetectorPixelY) """+ str((int(y))) +"""; -""","""set ::Xsetup_private(DGdx) """+ str(px) +"""; -""","""set ::Xsetup_private(DGdy) """+ str(px) +"""; -""","""set ::Xdetector(AutoD) {max}; -""","""set ::Xdetector(RefGV) 50000; -""","""::XDetector::UpdateGeometry 1; -"""] - return STR - -def aRTist_SETUP_source(pos, kV, mA): - STR = ["""set ::Xsetup(SourceSampling) {point}; -""","""set ::Xsource(Exposure) """+ str(mA) +"""; -""","""set ::Xsource(Tube) {Mono}; -""","""set ::Xsource(Voltage) """+ str(kV) +"""; -""","""::PartList::Invoke S SetPosition 0 0 """+ str(pos) +"""; -""","""::PartList::Invoke S SetRefPos 0 0 """+ str(pos) +"""; -""","""set ::Xdetector(FFCorrRun) 0; -""","""XDetector::FFCorrClearCmd; -""","""::XSource::spectrumOK; -"""] # set ::Engine::RenderPreview 0; - return STR - -def aRTist_SETUP_FFcorr(): - STR = ["""::XDetector::FFCorrGenCmd; -"""] - return STR - -def aRTist_create_sphere(R): - R = 2 * R - STR = ["""::Modules::Run Solid; -""","""set ::Modules::Module""" +str(SolidModNo)+"""::Solid(Type) {ellipsoid}; -""","""set ::Modules::Module""" +str(SolidModNo)+"""::Solid(Equilateral) 1; -""","""set ::Modules::Module""" +str(SolidModNo)+"""::Solid(X) """+ str(R) +"""; -""","""set ::Modules::Module""" +str(SolidModNo)+"""::Solid(PhiResolution) 80; -""","""set ::Modules::Module""" +str(SolidModNo)+"""::Solid(ThetaResolution) 80; -""","""set ::Modules::Module""" +str(SolidModNo)+"""::Solid(GridEllipsoid) 1; -""","""set ::Modules::Module""" +str(SolidModNo)+"""::Solid(VolumeCorrect) 1; -""","""::Modules::Module""" +str(SolidModNo)+"""::GenerateCmd; -"""] - return STR - -def aRTist_set_material(ID, mat): - STR = ["""::PartList::Set """+ str(ID) +""" Material """+ mat +"""; -"""] - return STR - -def aRTist_translate(ID, x, y, z): - STR = ["""::PartList::Invoke """+ str(ID) +""" SetPosition """+ str(x) +""" """+ str(y) +""" """+ str(z) +"""; -""","""::PartList::Invoke """+ str(ID) +""" SetRefPos """+ str(x) +""" """+ str(y) +""" """+ str(z) +"""; -"""] - return STR - -def aRTist_vis_off(): - STR = ["""::PartList::Set 1 Visible off; -""","""::PartList::Set 2 Visible off; -"""] - return STR - -def aRTist_vis_on(ID): - STR = ["""::PartList::Set """+str(ID)+""" Visible on; -"""] - return STR - -def aRTist_resize(ID, size): - STR = ["""::PartList::Invoke """+str(ID)+""" SetSize """+str(size)+""" """+str(size)+""" """+str(size)+"""; -"""] - return STR - -def aRTist_make_image(): - STR = ["""::Engine::StartStopCmd; -"""] - return STR - -def aRTist_save_image(Path): - STR = ["""::Modules::Execute ImageViewer Save16bit """+ Path +""" 1; -"""] - return STR - - -# def aRTist_fire(): - # STR = ["""::Modules::Module""" +str(SolidModNo)+"""::GenerateCmd; -# """] -# ::Modules::Module""" +str(SolidModNo)+"""::Close;" - # return STR - -########################## Conversions ################################ -''' Particle/Pore ''' -R_max = D_max / 2 / 1000 # max. particle radius in mm -R_min = D_min / 2 / 1000 # min. particle radius in mm -r_max = P_max / 2 / 1000 # max. pore radius in mm -r_min = P_min / 2 / 1000 # min. pore radius in mm - -''' Detector/Source ''' -OZ = SDD / MAG # position of object (in Z-direction) -OZ = SDD - OZ -VX = pitch / MAG # voxel size , i.e. eff. pixel size -DETxy = (DBorder * D_max) / (VX * 1000) # detector size (square) in pixel - -P_xy = (DETxy / 2) * VX * 0.9 # origin of particle range[x][y] with 10% border - -############################################################################### -''' Generation of random variables and calculate objects (paricles+pores) ''' -P_ID, P_RAD, P_XYZ, p_ANZ, p_RAD, p_XYZ = [],[],[],[],[],[] # List of all particles/pores -R = np.array(range(N_Par), dtype=np.float) -for i in range(N_Par): - R[i] = round(random.uniform(R_min, R_max),3) # particle radius in mm - X = round(random.uniform(-(P_xy-R[i]), (P_xy-R[i])),3) # particle position x - Y = round(random.uniform(-(P_xy-R[i]), (P_xy-R[i])),3) # particle position y - print('Particle',i ,' RADIUS =',R[i] ,'mm') - P_ID.append(i) - P_RAD.append(R[i]) - P_XYZ.append([X, Y, OZ]) - pores = random.randint(pores_min, pores_max) # random no. of pores - r = [] #np.array(range(pores), dtype=np.float) - p_xyz = [] - for ii in range(pores): - r.append(round(random.uniform(r_min, r_max),3)) # random pore radius in mm - print('Particle',i ,' Pore',ii ,' RADIUS =', r[ii],'mm') - - ''' Generate coordinates for pore ''' - R2 = round(R[i] - space - r[ii],3) # max. sphere radius with R2+pore in sphere R - # print(R2) - R3 = round(random.uniform(0, R2),3) # sphere with random radius in R2 - theta = random.uniform(0, math.pi) - phi = random.uniform(0, 2*math.pi) - # print(theta, phi) - p_x = round((X + R3 * math.sin(theta) * math.cos(phi)),3) - p_y = round((Y + R3 * math.sin(theta) * math.sin(phi)),3) - p_z = round((OZ + R3 * math.cos(theta)),3) - p_xyz.append([p_x, p_y, p_z]) - p_ANZ.append(pores) - p_RAD.append(r) - p_XYZ.append(p_xyz) - -print(P_RAD) -print(P_XYZ) -print(p_RAD) -print(p_XYZ) -print(p_ANZ) - -###################### Save coordinates in CSV ########################### -with open(path_save_images +"data.csv", "w+") as file: - STR = "Particle_ID, P_RADIUS, P_x, P_y, P_z, No. of pores, Pore_ID, p_RADIUS, p_x, p_y, p_z" - file.write(STR + "\n") - for i in range(N_Par): - STR = ""+str(P_ID[i])+", "+str(P_RAD[i])+", "+str(P_XYZ[i][0])+", "+str(P_XYZ[i][1])+", "+str(P_XYZ[i][2]) - if p_ANZ[i] == 0: - STR = STR + ", 0, , , , , " - file.write(STR + "\n") - elif p_ANZ[i] > 0: - STR = STR + ", " +str(p_ANZ[i]) - for ii in range(p_ANZ[i]): - STR2 = STR +", "+str(ii)+", "+str(p_RAD[i][ii])+", "+str(p_XYZ[i][ii][0])+", "+str(p_XYZ[i][ii][1])+", "+str(p_XYZ[i][ii][2]) - file.write(STR2 + "\n") - -############################################################################### -''' Connect to aRTist ''' -S = aRTist_connect() - -aRTist_listen(0) - -############################################################################### -''' SETUP aRTist scene ''' -print("SETUP aRTist scene") -aRTist_sent(aRTist_setup(path_aRTist_scene)) -print("SETUP Detector aRTist-Scene") -aRTist_sent(aRTist_SETUP_detector(DETxy, DETxy, pitch)) -print("SETUP Source aRTist-Scene") -aRTist_sent(aRTist_SETUP_source(SDD, kV, mA)) -print("SETUP FFcorr aRTist-Scene") -aRTist_sent(aRTist_SETUP_FFcorr()) -aRTist_sent(["""set ::Xdetector(FFCorrRun) 1; -"""]) -print("SETUP FINISH aRTist-Scene") - -############################################################################### -''' Create particles and pores in aRTist, save image ''' -# Create two dummy spheres -aRTist_sent(aRTist_create_sphere(R_max)) -aRTist_sent(aRTist_create_sphere(r_max)) -aRTist_sent(aRTist_set_material(1, "{Ti}")) -aRTist_sent(aRTist_set_material(2, "{void}")) -#aRTist_sent(["""::Modules::Module""" +str(SolidModNo)+"""::Close; -#"""]) - -# translate spheres -for i in range(N_Par): - # particle - print("Create Particle ", i , "of", N_Par) - aRTist_sent(aRTist_vis_off()) - aRTist_sent(aRTist_vis_on(1)) - aRTist_sent(aRTist_resize(1, (2*P_RAD[i]))) - aRTist_sent(aRTist_translate(1, P_XYZ[i][0], P_XYZ[i][1], P_XYZ[i][2])) - - # pores - if p_ANZ[i] > 0: - aRTist_sent(aRTist_vis_on(2)) - aRTist_sent(aRTist_resize(2, (2*p_RAD[i][0]))) - aRTist_sent(aRTist_translate(2, p_XYZ[i][0][0], p_XYZ[i][0][1], p_XYZ[i][0][2])) - # for ii in range(p_ANZ[i]): - # acquire image - aRTist_sent(aRTist_make_image()) - # save image - aRTist_sent(aRTist_save_image((path_save_images + str(i).zfill(5) +".tif"))) - - - -############################################################################### -''' Timer for Debug ''' -for i in range(5): - print("wait ",i ," s") - sleep(1) -print("FINISH!", error, "aRTist Errors") -############################################################################### -''' Close Connection to aRTist''' -S.close() diff --git a/Standalones/ParticlesAndPores/Pore_Matrix_Scene.aRTist b/Standalones/ParticlesAndPores/Pore_Matrix_Scene.aRTist deleted file mode 100644 index d2b7087..0000000 Binary files a/Standalones/ParticlesAndPores/Pore_Matrix_Scene.aRTist and /dev/null differ diff --git a/Standalones/ParticlesAndPores/Single_Pore_Scene.aRTist b/Standalones/ParticlesAndPores/Single_Pore_Scene.aRTist deleted file mode 100644 index 29ae4fe..0000000 Binary files a/Standalones/ParticlesAndPores/Single_Pore_Scene.aRTist and /dev/null differ diff --git a/artistlib/__init__.py b/artistlib/__init__.py deleted file mode 100644 index 2f8d6a7..0000000 --- a/artistlib/__init__.py +++ /dev/null @@ -1,125 +0,0 @@ -# -*- coding: UTF-8 -*- -"""The aRTist Python library is intended to remote control and automate the radiographic simulator aRTist. - -.. include:: ./documentation.md -""" - -__pdoc__ = {'console': False, 'remote_access': False} - -from ._version import get_versions -__version__ = get_versions()['version'] -del get_versions - -import numpy as np -from numpy import append -import socket -import base64 -import pathlib -from PIL import Image -class Junction: - """Remote control of aRTist simulator (this is a test) - """ - def __init__(self, host="localhost", port=3658, bufferSize=1024, timeout=5): - self.host = host - self.port = port - self.bufferSize = bufferSize - self.timeout = timeout - self.error = 0 - self.progress = 0 - self.answer = {} - - self.connect() - - def connect(self): - self.S = socket.socket() # Create socket (for TCP) - self.S.connect((self.host, self.port)) # Connect to aRTist - self.S.settimeout(self.timeout) - self.listen(0) - return self - - def send(self, command, msgType="RESULT"): - c = command + '\n' - self.S.send(c.encode()) - return self.listen(msgType=msgType) - - def listen(self, command_no=1, msgType="RESULT"): - answer = "" - stop = False - if (command_no == 0): - self.S.settimeout(0.2) - while (not stop):# and ("SUCCESS" not in total) and ("ERROR" not in total): # Solange server antwortet und nicht "SUCCESS" enthält - try: - msg = self.S.recv(self.bufferSize).decode() - except BaseException as e: - err = e.args[0] - if err == "timed out": - #print("Timeout\n") - answer += "RESULT Timeout\n" - #print(answer) - stop = True - continue - else: - if ("SUCCESS" in msg): - answer += msg - stop = True - continue - elif ("ERROR" in msg): - answer += msg - stop = True - #global error - self.error = self.error + 1 - continue - elif ("PROGRESS" in msg): - try: - self.progress = float(msg.strip('PROGRESS ')) - except: - self.progress = 0 - continue - else: - if (command_no == 0): - print(msg) - answer += msg - self.S.settimeout(self.timeout) - self.answer.update({"SUCCESS":self.pick(answer, "SUCCESS"), "RESULT":self.pick(answer, "RESULT"), "SDTOUT":self.pick(answer, "STDOUT"), "BASE64":self.pick(answer, "BASE64"), "IMAGE":self.pick(answer, "IMAGE"), "FILE":self.pick(answer, "FILE")}) - if (msgType != "*"): - answer = self.pick(answer, msgType) - return answer - - def pick(self, answer, res='RESULT'): - picked = '' - for a in answer.split('\n'): - if a.find(res) == 0: - picked += a[1 + len(res):].strip('\r') + '\n' - if len(picked) == 0: - return res + ' not found.' - return picked - - def get_answer(self, key): - return self.answer[key] - - def save_image(self, imageName): - npTypes = [np.bool_, np.ubyte, np.byte, np.ubyte, np.short, np.ushort, np.intc, np.uintc, np.int_, np.uint, np.single, np.double] - imageData = self.answer["BASE64"] - decodedData = base64.b64decode((imageData)) - imageHeader = self.answer["IMAGE"].split() - dtype = npTypes[int(imageHeader[4])] - im = np.frombuffer(decodedData, dtype).reshape((int(imageHeader[1]),int(imageHeader[0]))) - Image.fromarray(im).save(imageName) - - def receive_file(self, fileName): - fileData = self.answer["BASE64"] - decodedFile = base64.b64decode((fileData)) - artistFile = open(fileName, "wb") - artistFile.write(decodedFile) - artistFile.close() - - def send_file(self, fileName): - outFile = open(fileName, "br") - fileBytes = outFile.read() - encBytes = base64.b64encode((fileBytes)) - encString = str(encBytes) - encString = encString.lstrip("b'").rstrip("'") - fileExtension = pathlib.Path(fileName).suffix - com = "::RemoteControl::ReceiveFile " + encString + " " + fileExtension - recAnswer = self.send(com, "RESULT") - return recAnswer diff --git a/artistlib/_version.py b/artistlib/_version.py deleted file mode 100644 index 6e093b4..0000000 --- a/artistlib/_version.py +++ /dev/null @@ -1,658 +0,0 @@ - -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. -# Generated by versioneer-0.26 -# https://github.com/python-versioneer/python-versioneer - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys -from typing import Callable, Dict -import functools - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "$Format:%d$" - git_full = "$Format:%H$" - git_date = "$Format:%ci$" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "pep440" - cfg.tag_prefix = "v" - cfg.parentdir_prefix = "" - cfg.versionfile_source = "artistlib/_version.py" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs, method): # decorator - """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen([command] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None), **popen_kwargs) - break - except OSError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, process.returncode - return stdout, process.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %s but none started with prefix %s" % - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r'\d', r)} - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r'\d', r): - continue - if verbose: - print("picking %s" % r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner(GITS, [ - "describe", "--tags", "--dirty", "--always", "--long", - "--match", f"{tag_prefix}[[:digit:]]*" - ], cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], - cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%s'" - % describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = ("tag '%s' doesn't start with prefix '%s'" - % (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces): - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver): - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces): - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%d" % (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for _ in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} diff --git a/artistlib/console.py b/artistlib/console.py deleted file mode 100644 index 22a9aa0..0000000 --- a/artistlib/console.py +++ /dev/null @@ -1,7 +0,0 @@ -import subprocess -import os - -path = os.path.dirname(os.path.abspath(__file__)) -correctedPath = path.replace("\\", "/") - -cmd = subprocess.run(["python", correctedPath + "/remote_access.py"]) \ No newline at end of file diff --git a/artistlib/documentation.md b/artistlib/documentation.md deleted file mode 100644 index f1749aa..0000000 --- a/artistlib/documentation.md +++ /dev/null @@ -1,65 +0,0 @@ -**Hint:** This project is in its early stages and may change significantly over time. - -Getting started -=============== - -Requirements ------------- -A **Python 3** environment (Python 3.8 or higher) is required. The following Python packages are required as well. They usually come with a Python environment, or can be installed there easily: - -* none so far. - - -Installation ------------- - -If you want to **install** the package in your Python environment, you can use [pip]. For example, you can run the following command to make the toolbox available: - - pip install artistlib - -[pip]: https://pip.pypa.io - -To use the package **without installation**, you need to download the package manually. You have the following three options: - -* Download the package [from PyPi]. You will get a zipped file called `artistlib-X.X.X.tar.gz` (where X.X.X is the current version number). Open or unpack this file to get to its contents. -* Download the repository [from GitHub]: press the *clone* button to download a ZIP file. Unpack it or open it to see its contents. -* You can also clone the repository from GitHub via the terminal: - - `git clone https://github.com/BAMresearch/aRTist-PythonLib.git` - -From any of these three options, you will get the complete package source code. It contains a folder called `artistlib`. If you want to use the library from your Python scripts without installing it, you need to copy the folder `artistlib` to the location of your Python scripts to make the package available. - - -[from GitHub]: https://github.com/BAMresearch/aRTist-PythonLib -[from PyPi]: https://pypi.org/project/artistlib/ - -Usage ------ - -Please make sure that aRTist is running and waiting for remote connection (menu: Tools>Enable remote access). - -The following example code shows the basic usage: - -```python -.. include:: ../example_artistlib.py -``` - -About -===== - -The aRTist library was developed for utilize the Python scripting of the radiographic simulator [aRTist]. - -The software is released under the **Apache 2.0 license,** its source code is available [on GitHub]. - -[aRTist]: https://artist.bam.de -[on GitHub]: https://github.com/BAMresearch/aRTist-PythonLib - -Contributors ------------- -The following people contributed to code and documentation of the package: - -* Alexander Funke -* David Schumacher -* Carsten Bellon -* David Plotzki -* David Denkler \ No newline at end of file diff --git a/artistlib/remote_access.py b/artistlib/remote_access.py deleted file mode 100644 index 06c8876..0000000 --- a/artistlib/remote_access.py +++ /dev/null @@ -1,56 +0,0 @@ -import sys -import os -path = os.path.dirname(os.path.abspath(__file__)) -path = os.path.dirname(path) -sys.path.insert(0, path) - -import artistlib as a -from prompt_toolkit import PromptSession -session = PromptSession() - -list = ["SUCCESS", "RESULT", "STDOUT"] -commands = [] - -rc = a.Junction() - -c = 0 - -while True: - try: - com = session.prompt("Command: ") - - if "::RemoteControl::ReceiveFile" in com: - fileName2 = input("Send following file: ") - recAnswer = a.Junction.send_file(rc, fileName2) - print(recAnswer) - - else: - ans = a.Junction.send(rc, com, "*") - - if "FILE" in ans: - fileName = input("Save file as: ") - a.Junction.receive_file(rc, fileName) - print("File saved as ", fileName) - - for i in list: - typ = a.Junction.pick(rc, ans, i) - if "IMAGE" in ans and not "{}" in typ: - name = input("Save Image as: ") - a.Junction.save_image(rc, name) - print("Image saved as ", name) - - if not "{}" in typ: - if not "not found" in typ: - print(typ) - else: - c += 1 - else: - c += 1 - - if c >= 3 and not "BASE64" in ans: - print(ans) - - c = 0 - - except KeyboardInterrupt: - raise SystemExit diff --git a/build.sh b/build.sh deleted file mode 100644 index dcd830f..0000000 --- a/build.sh +++ /dev/null @@ -1,6 +0,0 @@ -#!/bin/bash -rm -R dist -rm -R artistlib.egg-info -python -m build - -# twine upload dist/* \ No newline at end of file diff --git a/build_html.sh b/build_html.sh deleted file mode 100644 index 18e650d..0000000 --- a/build_html.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash -# Builds the HTML documentation using pdoc3 -# and moves it to the "docs" folder (instead of docs/artistlib). -pdoc --force --html --template-dir "docs/templates" -o "docs/" artistlib -cp -R docs/artistlib/* docs/ -rm -R docs/artistlib -###pdoc --logo "artistlib.png" --template-dir "docs/templates" -o "docs/" artistlib -###rm -R docs/artistlib \ No newline at end of file diff --git a/build_pdf.sh b/build_pdf.sh deleted file mode 100644 index 34c26c2..0000000 --- a/build_pdf.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash -# Builds the documentation as a PDF file, -# using pdoc3 to create a complete Markdown file, -# which is then passed to pandoc to create a LaTeX -# file and a PDF using XeLaTeX. -pdoc --force --pdf artistlib > docs/artistlib.md -pandoc --metadata=title:"aRTsit PythonLib Documentation" --from=markdown+abbreviations+tex_math_single_backslash --pdf-engine=xelatex --variable=mainfont:"DejaVu Sans" --toc --toc-depth=1 --output=docs/artistlib.pdf docs/artistlib.md -rm docs/artistlib.md \ No newline at end of file diff --git a/docs/artistlib.png b/docs/artistlib.png deleted file mode 100644 index 18bf79c..0000000 Binary files a/docs/artistlib.png and /dev/null differ diff --git a/docs/favicon.ico b/docs/favicon.ico deleted file mode 100644 index ae77cce..0000000 Binary files a/docs/favicon.ico and /dev/null differ diff --git a/docs/index.html b/docs/index.html deleted file mode 100644 index fc818e1..0000000 --- a/docs/index.html +++ /dev/null @@ -1,579 +0,0 @@ - - - - - - -artistlib API documentation - - - - - - - - - - - - - -
-
-
-

Package artistlib

-
-
-

The aRTist Python library is intended to remote control and automate the radiographic simulator aRTist.

-

Hint: This project is in its early stages and may change significantly over time.

-

Getting started

-

Requirements

-

A Python 3 environment (Python 3.8 or higher) is required. The following Python packages are required as well. They usually come with a Python environment, or can be installed there easily:

-
    -
  • none so far.
    • -
-

Installation

-

If you want to install the package in your Python environment, you can use pip. For example, you can run the following command to make the toolbox available:

-
pip install artistlib
-
-

To use the package without installation, you need to download the package manually. You have the following three options:

-
    -
  • Download the package from PyPi. You will get a zipped file called artistlib-X.X.X.tar.gz (where X.X.X is the current version number). Open or unpack this file to get to its contents.
    • -
  • Download the repository from GitHub: press the clone button to download a ZIP file. Unpack it or open it to see its contents.
    • -
  • -

    You can also clone the repository from GitHub via the terminal:

    -

    git clone https://github.com/BAMresearch/aRTist-PythonLib.git

    -
    • -
-

From any of these three options, you will get the complete package source code. It contains a folder called artistlib. If you want to use the library from your Python scripts without installing it, you need to copy the folder artistlib to the location of your Python scripts to make the package available.

-

Usage

-

Please make sure that aRTist is running and waiting for remote connection (menu: Tools>Enable remote access).

-

The following example code shows the basic usage:

-
import artistlib as a
-
-# connect to aRTist (default: host='localhost', port=3658) 
-rc = a.Junction()
-
-# print aRTist's version number
-ver = a.Junction.send(rc, '::aRTist::GetVersion full')
-print(ver)
-
-# - load a project
-# - run the simulation
-# - save the resulting projection from the image viewer
-a.Junction.send(rc, 'FileIO::OpenAny $Xray(LibraryDir)/ExampleProjects/Schlumpfmark.aRTist')
-a.Junction.send(rc, 'Engine::GoCmd')
-ans = "Saved as: "
-ans += a.Junction.send(rc, 'Modules::Invoke ImageViewer SaveFile [file join $env(HOME) Pictures/artistlib.tif] true')
-print(ans)
-
-# - load a project
-# - run the simulation without viewing the result
-# - transfer the final projection 
-# - saving the projection image  >>>> This requires aRTist 2.12.7 or higher! <<<<
-# - delete the images to release the memory
-a.Junction.send(rc, 'FileIO::OpenAny $Xray(LibraryDir)/ExampleProjects/aRTist.aRTist')
-a.Junction.send(rc, 'set imgList [Engine::Go]')
-a.Junction.send(rc, 'RemoteControl::SendImage [lindex $imgList 0]')
-a.Junction.save_image(rc, "transferred.tif")
-a.Junction.send(rc, 'foreach i $imgList {$i Delete}')
-print("Saved as: transferred.tif")
-
-

About

-

The aRTist library was developed for utilize the Python scripting of the radiographic simulator aRTist.

-

The software is released under the Apache 2.0 license, its source code is available on GitHub.

-

Contributors

-

The following people contributed to code and documentation of the package:

-
    -
  • Alexander Funke
    • -
  • David Schumacher
    • -
  • Carsten Bellon
    • -
  • David Plotzki
    • -
  • David Denkler
    • -
-
- -Expand source code - -
# -*- coding: UTF-8 -*-
-"""The aRTist Python library is intended to remote control and automate the radiographic simulator aRTist.
-
-.. include:: ./documentation.md
-"""
-
-__pdoc__ = {'console': False, 'remote_access': False}
-
-from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
-
-import numpy as np
-from numpy import append
-import socket
-import base64
-import pathlib
-from PIL import Image
-class Junction:
-    """Remote control of aRTist simulator (this is a test)
-    """
-    def __init__(self, host="localhost", port=3658, bufferSize=1024, timeout=5):
-        self.host = host
-        self.port = port
-        self.bufferSize = bufferSize
-        self.timeout = timeout
-        self.error = 0
-        self.progress = 0
-        self.answer = {}
-
-        self.connect()
-
-    def connect(self):
-        self.S = socket.socket()                        # Create socket (for TCP)
-        self.S.connect((self.host, self.port))          # Connect to aRTist
-        self.S.settimeout(self.timeout)
-        self.listen(0)
-        return self
-
-    def send(self, command, msgType="RESULT"):
-        c = command + '\n'
-        self.S.send(c.encode())
-        return self.listen(msgType=msgType)
-
-    def listen(self, command_no=1, msgType="RESULT"):
-        answer = ""
-        stop = False
-        if (command_no == 0):
-            self.S.settimeout(0.2)
-        while (not stop):# and ("SUCCESS" not in total) and ("ERROR" not in total):     # Solange server antwortet und nicht "SUCCESS" enthält
-            try:
-                msg = self.S.recv(self.bufferSize).decode()
-            except BaseException as e:
-                err = e.args[0]
-                if err == "timed out":
-                    #print("Timeout\n")
-                    answer += "RESULT Timeout\n"
-                    #print(answer)
-                    stop = True
-                    continue
-            else:
-                if ("SUCCESS" in msg):
-                    answer += msg
-                    stop = True
-                    continue
-                elif ("ERROR" in msg):
-                    answer += msg
-                    stop = True
-                    #global error
-                    self.error = self.error + 1 
-                    continue
-                elif ("PROGRESS" in msg):
-                    try:
-                        self.progress = float(msg.strip('PROGRESS '))
-                    except:
-                        self.progress = 0
-                    continue
-                else:
-                    if (command_no == 0):
-                        print(msg)
-                    answer += msg
-        self.S.settimeout(self.timeout)
-        self.answer.update({"SUCCESS":self.pick(answer, "SUCCESS"), "RESULT":self.pick(answer, "RESULT"), "SDTOUT":self.pick(answer, "STDOUT"), "BASE64":self.pick(answer, "BASE64"), "IMAGE":self.pick(answer, "IMAGE"), "FILE":self.pick(answer, "FILE")})
-        if (msgType != "*"):
-            answer = self.pick(answer, msgType)
-        return answer
-
-    def pick(self, answer, res='RESULT'):
-        picked = ''
-        for a in answer.split('\n'):
-            if a.find(res) == 0:
-                picked += a[1 + len(res):].strip('\r') + '\n'
-        if len(picked) == 0:
-            return res + ' not found.'
-        return picked
-
-    def get_answer(self, key):
-        return self.answer[key]
-
-    def save_image(self, imageName):
-        npTypes = [np.bool_, np.ubyte, np.byte, np.ubyte, np.short, np.ushort, np.intc, np.uintc, np.int_, np.uint, np.single, np.double]
-        imageData = self.answer["BASE64"]
-        decodedData = base64.b64decode((imageData))
-        imageHeader = self.answer["IMAGE"].split()
-        dtype = npTypes[int(imageHeader[4])]
-        im = np.frombuffer(decodedData, dtype).reshape((int(imageHeader[1]),int(imageHeader[0])))
-        Image.fromarray(im).save(imageName)
-
-    def receive_file(self, fileName):
-        fileData = self.answer["BASE64"]
-        decodedFile = base64.b64decode((fileData))
-        artistFile = open(fileName, "wb")
-        artistFile.write(decodedFile)
-        artistFile.close()
-
-    def send_file(self, fileName):
-        outFile = open(fileName, "br")
-        fileBytes = outFile.read()
-        encBytes = base64.b64encode((fileBytes))
-        encString = str(encBytes)
-        encString = encString.lstrip("b'").rstrip("'")
-        fileExtension = pathlib.Path(fileName).suffix
-        com = "::RemoteControl::ReceiveFile " + encString + " " + fileExtension
-        recAnswer = self.send(com, "RESULT")
-        return recAnswer
-
-
-
-
-
-
-
-
-
-

Classes

-
-
-class Junction -(host='localhost', port=3658, bufferSize=1024, timeout=5) -
-
-

Remote control of aRTist simulator (this is a test)

-
- -Expand source code - -
class Junction:
-    """Remote control of aRTist simulator (this is a test)
-    """
-    def __init__(self, host="localhost", port=3658, bufferSize=1024, timeout=5):
-        self.host = host
-        self.port = port
-        self.bufferSize = bufferSize
-        self.timeout = timeout
-        self.error = 0
-        self.progress = 0
-        self.answer = {}
-
-        self.connect()
-
-    def connect(self):
-        self.S = socket.socket()                        # Create socket (for TCP)
-        self.S.connect((self.host, self.port))          # Connect to aRTist
-        self.S.settimeout(self.timeout)
-        self.listen(0)
-        return self
-
-    def send(self, command, msgType="RESULT"):
-        c = command + '\n'
-        self.S.send(c.encode())
-        return self.listen(msgType=msgType)
-
-    def listen(self, command_no=1, msgType="RESULT"):
-        answer = ""
-        stop = False
-        if (command_no == 0):
-            self.S.settimeout(0.2)
-        while (not stop):# and ("SUCCESS" not in total) and ("ERROR" not in total):     # Solange server antwortet und nicht "SUCCESS" enthält
-            try:
-                msg = self.S.recv(self.bufferSize).decode()
-            except BaseException as e:
-                err = e.args[0]
-                if err == "timed out":
-                    #print("Timeout\n")
-                    answer += "RESULT Timeout\n"
-                    #print(answer)
-                    stop = True
-                    continue
-            else:
-                if ("SUCCESS" in msg):
-                    answer += msg
-                    stop = True
-                    continue
-                elif ("ERROR" in msg):
-                    answer += msg
-                    stop = True
-                    #global error
-                    self.error = self.error + 1 
-                    continue
-                elif ("PROGRESS" in msg):
-                    try:
-                        self.progress = float(msg.strip('PROGRESS '))
-                    except:
-                        self.progress = 0
-                    continue
-                else:
-                    if (command_no == 0):
-                        print(msg)
-                    answer += msg
-        self.S.settimeout(self.timeout)
-        self.answer.update({"SUCCESS":self.pick(answer, "SUCCESS"), "RESULT":self.pick(answer, "RESULT"), "SDTOUT":self.pick(answer, "STDOUT"), "BASE64":self.pick(answer, "BASE64"), "IMAGE":self.pick(answer, "IMAGE"), "FILE":self.pick(answer, "FILE")})
-        if (msgType != "*"):
-            answer = self.pick(answer, msgType)
-        return answer
-
-    def pick(self, answer, res='RESULT'):
-        picked = ''
-        for a in answer.split('\n'):
-            if a.find(res) == 0:
-                picked += a[1 + len(res):].strip('\r') + '\n'
-        if len(picked) == 0:
-            return res + ' not found.'
-        return picked
-
-    def get_answer(self, key):
-        return self.answer[key]
-
-    def save_image(self, imageName):
-        npTypes = [np.bool_, np.ubyte, np.byte, np.ubyte, np.short, np.ushort, np.intc, np.uintc, np.int_, np.uint, np.single, np.double]
-        imageData = self.answer["BASE64"]
-        decodedData = base64.b64decode((imageData))
-        imageHeader = self.answer["IMAGE"].split()
-        dtype = npTypes[int(imageHeader[4])]
-        im = np.frombuffer(decodedData, dtype).reshape((int(imageHeader[1]),int(imageHeader[0])))
-        Image.fromarray(im).save(imageName)
-
-    def receive_file(self, fileName):
-        fileData = self.answer["BASE64"]
-        decodedFile = base64.b64decode((fileData))
-        artistFile = open(fileName, "wb")
-        artistFile.write(decodedFile)
-        artistFile.close()
-
-    def send_file(self, fileName):
-        outFile = open(fileName, "br")
-        fileBytes = outFile.read()
-        encBytes = base64.b64encode((fileBytes))
-        encString = str(encBytes)
-        encString = encString.lstrip("b'").rstrip("'")
-        fileExtension = pathlib.Path(fileName).suffix
-        com = "::RemoteControl::ReceiveFile " + encString + " " + fileExtension
-        recAnswer = self.send(com, "RESULT")
-        return recAnswer
-
-

Methods

-
-
-def connect(self) -
-
-
-
- -Expand source code - -
def connect(self):
-    self.S = socket.socket()                        # Create socket (for TCP)
-    self.S.connect((self.host, self.port))          # Connect to aRTist
-    self.S.settimeout(self.timeout)
-    self.listen(0)
-    return self
-
-
-
-def get_answer(self, key) -
-
-
-
- -Expand source code - -
def get_answer(self, key):
-    return self.answer[key]
-
-
-
-def listen(self, command_no=1, msgType='RESULT') -
-
-
-
- -Expand source code - -
def listen(self, command_no=1, msgType="RESULT"):
-    answer = ""
-    stop = False
-    if (command_no == 0):
-        self.S.settimeout(0.2)
-    while (not stop):# and ("SUCCESS" not in total) and ("ERROR" not in total):     # Solange server antwortet und nicht "SUCCESS" enthält
-        try:
-            msg = self.S.recv(self.bufferSize).decode()
-        except BaseException as e:
-            err = e.args[0]
-            if err == "timed out":
-                #print("Timeout\n")
-                answer += "RESULT Timeout\n"
-                #print(answer)
-                stop = True
-                continue
-        else:
-            if ("SUCCESS" in msg):
-                answer += msg
-                stop = True
-                continue
-            elif ("ERROR" in msg):
-                answer += msg
-                stop = True
-                #global error
-                self.error = self.error + 1 
-                continue
-            elif ("PROGRESS" in msg):
-                try:
-                    self.progress = float(msg.strip('PROGRESS '))
-                except:
-                    self.progress = 0
-                continue
-            else:
-                if (command_no == 0):
-                    print(msg)
-                answer += msg
-    self.S.settimeout(self.timeout)
-    self.answer.update({"SUCCESS":self.pick(answer, "SUCCESS"), "RESULT":self.pick(answer, "RESULT"), "SDTOUT":self.pick(answer, "STDOUT"), "BASE64":self.pick(answer, "BASE64"), "IMAGE":self.pick(answer, "IMAGE"), "FILE":self.pick(answer, "FILE")})
-    if (msgType != "*"):
-        answer = self.pick(answer, msgType)
-    return answer
-
-
-
-def pick(self, answer, res='RESULT') -
-
-
-
- -Expand source code - -
def pick(self, answer, res='RESULT'):
-    picked = ''
-    for a in answer.split('\n'):
-        if a.find(res) == 0:
-            picked += a[1 + len(res):].strip('\r') + '\n'
-    if len(picked) == 0:
-        return res + ' not found.'
-    return picked
-
-
-
-def receive_file(self, fileName) -
-
-
-
- -Expand source code - -
def receive_file(self, fileName):
-    fileData = self.answer["BASE64"]
-    decodedFile = base64.b64decode((fileData))
-    artistFile = open(fileName, "wb")
-    artistFile.write(decodedFile)
-    artistFile.close()
-
-
-
-def save_image(self, imageName) -
-
-
-
- -Expand source code - -
def save_image(self, imageName):
-    npTypes = [np.bool_, np.ubyte, np.byte, np.ubyte, np.short, np.ushort, np.intc, np.uintc, np.int_, np.uint, np.single, np.double]
-    imageData = self.answer["BASE64"]
-    decodedData = base64.b64decode((imageData))
-    imageHeader = self.answer["IMAGE"].split()
-    dtype = npTypes[int(imageHeader[4])]
-    im = np.frombuffer(decodedData, dtype).reshape((int(imageHeader[1]),int(imageHeader[0])))
-    Image.fromarray(im).save(imageName)
-
-
-
-def send(self, command, msgType='RESULT') -
-
-
-
- -Expand source code - -
def send(self, command, msgType="RESULT"):
-    c = command + '\n'
-    self.S.send(c.encode())
-    return self.listen(msgType=msgType)
-
-
-
-def send_file(self, fileName) -
-
-
-
- -Expand source code - -
def send_file(self, fileName):
-    outFile = open(fileName, "br")
-    fileBytes = outFile.read()
-    encBytes = base64.b64encode((fileBytes))
-    encString = str(encBytes)
-    encString = encString.lstrip("b'").rstrip("'")
-    fileExtension = pathlib.Path(fileName).suffix
-    com = "::RemoteControl::ReceiveFile " + encString + " " + fileExtension
-    recAnswer = self.send(com, "RESULT")
-    return recAnswer
-
-
-
-
-
-
-
- -
- - - \ No newline at end of file diff --git a/docs/templates/head.mako b/docs/templates/head.mako deleted file mode 100644 index 9897e5a..0000000 --- a/docs/templates/head.mako +++ /dev/null @@ -1,25 +0,0 @@ -<%! - from pdoc.html_helpers import minify_css -%> -<%def name="homelink()" filter="minify_css"> - .homelink { - display: block; - font-size: 2em; - font-weight: bold; - color: #555; - padding-bottom: .5em; - border-bottom: 1px solid silver; - } - .homelink:hover { - color: inherit; - } - .homelink img { - max-width:35%; - max-height: 5em; - margin: auto; - margin-bottom: .3em; - } - - - - diff --git a/docs/templates/logo.mako b/docs/templates/logo.mako deleted file mode 100644 index a327aae..0000000 --- a/docs/templates/logo.mako +++ /dev/null @@ -1,5 +0,0 @@ -
- - artistlib - -
diff --git a/docs/test.html b/docs/test.html deleted file mode 100644 index 0fe9040..0000000 --- a/docs/test.html +++ /dev/null @@ -1,5 +0,0 @@ - - - This is a second test! - - diff --git a/example_artistlib.py b/example_artistlib.py deleted file mode 100644 index e81a6da..0000000 --- a/example_artistlib.py +++ /dev/null @@ -1,29 +0,0 @@ -import artistlib as a - -# connect to aRTist (default: host='localhost', port=3658) -rc = a.Junction() - -# print aRTist's version number -ver = a.Junction.send(rc, '::aRTist::GetVersion full') -print(ver) - -# - load a project -# - run the simulation -# - save the resulting projection from the image viewer -a.Junction.send(rc, 'FileIO::OpenAny $Xray(LibraryDir)/ExampleProjects/Schlumpfmark.aRTist') -a.Junction.send(rc, 'Engine::GoCmd') -ans = "Saved as: " -ans += a.Junction.send(rc, 'Modules::Invoke ImageViewer SaveFile [file join $env(HOME) Pictures/artistlib.tif] true') -print(ans) - -# - load a project -# - run the simulation without viewing the result -# - transfer the final projection -# - saving the projection image >>>> This requires aRTist 2.12.7 or higher! <<<< -# - delete the images to release the memory -a.Junction.send(rc, 'FileIO::OpenAny $Xray(LibraryDir)/ExampleProjects/aRTist.aRTist') -a.Junction.send(rc, 'set imgList [Engine::Go]') -a.Junction.send(rc, 'RemoteControl::SendImage [lindex $imgList 0]') -a.Junction.save_image(rc, "transferred.tif") -a.Junction.send(rc, 'foreach i $imgList {$i Delete}') -print("Saved as: transferred.tif") \ No newline at end of file diff --git a/examples/01_api_example.py b/examples/01_api_example.py new file mode 100644 index 0000000..102cb52 --- /dev/null +++ b/examples/01_api_example.py @@ -0,0 +1,76 @@ +# Copyright 2023 Simon Wittl (Deggendorf Institute of Technology) +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +import matplotlib.pyplot as plt +from pathlib import Path + +from artist_pythonlib import API +from artist_pythonlib.hardware import XraySource, XrayDetector + + +def main(): + # Initialize the api. + artist_api = API() + + # Move and rotate source to initial position / orientation. + artist_api.rotate('S', alpha=0., beta=77, gamma=-12.) + artist_api.translate('S', x=10, y=-129, z=199.4) + + # Get the current position of the source: + source_position = artist_api.get_position('S') + source_orientation = artist_api.get_orientation('S') + + print(f'Source Position: {source_position}') + print(f'Source Orientation: {source_orientation}') + + # Create a source object and set the voltage + source = XraySource() + source.voltage_kv = 142. + source.exposure_ma = 10. + + print(f'Source Voltage: {source.voltage_kv} kV') + print(f'Source Exposure: {source.exposure_ma} mA') + print(f'Source Type: {source.source_type}') + + # Create a detector object and set the resolution + detector = XrayDetector() + detector.detector_resolution_mm = [0.1, 0.15] + detector.detector_count_px = [1000, 1000] + + print(f'Detector Resolution: {detector.detector_resolution_mm} mm') + print(f'Detector Pixel Count: {detector.detector_count_px} px') + + # Load .stl part + new_id = artist_api.load_part( + Path(r'C:\Program Files\BAM\aRTist 2.12\Data\Library\ExampleParts\Fun\Dog.stl'), # Plesas check where the aRTist software is installed. + 'Fe', + 'test_object') + + # Make a projection an visualize it in python + image = artist_api.get_image() + + # change material + artist_api.set_material(new_id, 'Al') + + plt.imshow(image) + plt.show() + + # Set visibility off + artist_api.set_visibility(new_id, False) + + # Delete part + artist_api.delete_part(new_id) + +if __name__ == '__main__': + main() diff --git a/examples/02_circular_trajectory.py b/examples/02_circular_trajectory.py new file mode 100644 index 0000000..6e196ff --- /dev/null +++ b/examples/02_circular_trajectory.py @@ -0,0 +1,44 @@ +# Copyright 2023 Simon Wittl (Deggendorf Institute of Technology) +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +from __future__ import annotations + +from pathlib import Path + +from artist_pythonlib import API, PROJECTIONGEOMETRIES +from artist_pythonlib.trajectory import circular_trajectory + + +NUMBER_OF_PROJECTIONS = 20 +SAVEFOLDER = Path('./workspace') / 'example_02' +SAVEFOLDER.mkdir(exist_ok=True) + + +def main(): + trajectory = circular_trajectory(500., 1000., NUMBER_OF_PROJECTIONS) + api = API() + + for i in range(NUMBER_OF_PROJECTIONS): + source, detector, rotation_matrix = trajectory[0][i], trajectory[1][i], trajectory[2][i] + + api.translate('S', *source) + api.translate('D', *detector) + api.rotate_from_rotation_matrix('S', rotation_matrix) + api.rotate_from_rotation_matrix('D', rotation_matrix) + + api.save_image(SAVEFOLDER / f'{i:03}.tif', save_projection_geometry=PROJECTIONGEOMETRIES.THD) + + +if __name__ == '__main__': + main() + \ No newline at end of file diff --git a/examples/03_get_spectrum.py b/examples/03_get_spectrum.py new file mode 100644 index 0000000..00ffdcb --- /dev/null +++ b/examples/03_get_spectrum.py @@ -0,0 +1,51 @@ +from artist_pythonlib import API +import numpy as np +from matplotlib import pyplot as plt +from xraydb import mu_elam + + +def scrap_spectrum(artist_spectrum: str): + try: + spectrum_dict = artist_spectrum.split('# [degrees]} ')[1].split('{# Avg:')[0] + spectrum_dict = spectrum_dict.replace('{', '') + spectrum_dict = spectrum_dict.replace('}', '') + spectrum_dict = spectrum_dict.replace('\t', ' ') + spectrum_dict = spectrum_dict.split(' ')[:-1] + spectrum = np.array(spectrum_dict, np.float32) + return spectrum.reshape((-1, 2)) + except IndexError: + raise ValueError('Ploychromatic Source must be set in aRTist!') + + +def get_current_artist_spcectrum(api: API) -> np.ndarray: + return scrap_spectrum(api.rc.send('[Engine::GetSpectrum]')) + + +def main(): + api = API() + current_spectrum = get_current_artist_spcectrum(api) + energy_keV = current_spectrum[:, 0] + photons_n = current_spectrum[:, 1] + + plt.plot(energy_keV, photons_n) + plt.title('aRTist Source Spectrum') + plt.ylabel('Photons (n)') + plt.xlabel('Energy (keV)') + plt.show() + + energy = np.arange(500, 120000, 10) # energy in eV + + for elem in ('C', 'Cu', 'Au'): + mu = mu_elam(elem, energy) + plt.plot(energy / 1000., mu, label=elem) + + plt.title('X-ray Mass Attenuation') + plt.xlabel('Energy (keV)') + plt.ylabel(r'$\mu/\rho \rm\, (cm^2/gr)$') + plt.legend() + plt.yscale('log') + plt.xscale('log') + plt.show() + +if __name__ == '__main__': + main() \ No newline at end of file diff --git a/examples/04_save_image.py b/examples/04_save_image.py new file mode 100644 index 0000000..aa34c15 --- /dev/null +++ b/examples/04_save_image.py @@ -0,0 +1,17 @@ +from artist_pythonlib import SAVEMODES, API +from artist_pythonlib.common_types import PROJECTIONGEOMETRIES +from pathlib import Path + +def main(): + # Initialize the api. + artist_api = API() + + # Save Folder + save_folder = Path('./workspace') + save_folder.mkdir(exist_ok=True) + + # Save image / Save images and load them is fastern than to send the images via the rc connection. + artist_api.save_image(save_folder / 'projection.tif', SAVEMODES.UINT16, save_projection_geometry=PROJECTIONGEOMETRIES.THD) + +if __name__ == '__main__': + main() \ No newline at end of file diff --git a/project.toml b/project.toml deleted file mode 100644 index f56da58..0000000 --- a/project.toml +++ /dev/null @@ -1,7 +0,0 @@ -[build-system] -requires = [ - "setuptools>=42", - "versioneer" - "wheel" -] -build-backend = "setuptools.build_meta" diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..82a88c7 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,29 @@ +[project] +name = "artist-pythonlib" +version = "0.1.0" +description = "Add your description here" +readme = "README.md" +authors = [ + { name = "swittl", email = "simon.wittl@th-deg.de" } +] +requires-python = ">=3.10" +dependencies = [ + "matplotlib>=3.9.2", + "numpy>=2.1.3", + "pillow>=11.0.0", + "scipy>=1.14.1", + "thd-json>=0.1.0", + "xraydb>=4.5.4", +] + +[project.optional-dependencies] +thd = [ + "thd-json", +] + +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[tool.uv.sources] +thd-json = { git = "https://mygit.th-deg.de/roboct/definitions/json_schemas" } diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index f81c5e6..0000000 --- a/setup.cfg +++ /dev/null @@ -1,12 +0,0 @@ - -# See the docstring in versioneer.py for instructions. Note that you must -# re-run 'versioneer.py setup' after changing this section, and commit the -# resulting files. - -[versioneer] -VCS = git -style = pep440 -versionfile_source = artistlib/_version.py -versionfile_build = artistlib/_version.py -tag_prefix = v -parentdir_prefix = diff --git a/setup.py b/setup.py deleted file mode 100644 index 2aa7607..0000000 --- a/setup.py +++ /dev/null @@ -1,26 +0,0 @@ -from setuptools import setup -import versioneer - -with open("README.md", "r", encoding="utf-8") as fh: - long_description = fh.read() - -setup(name='artistlib', - version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), - description='aRTist Python library', - url='https://github.com/BAMresearch/aRTist-PythonLib', - author='Carsten Bellon', - author_email='Carsten.Bellon@bam.de', - long_description=long_description, - long_description_content_type="text/markdown", - license='Apache 2.0', - packages=['artistlib'], - classifiers=[ - "Programming Language :: Python :: 3", - "License :: OSI Approved :: Apache Software License", - "Operating System :: OS Independent", - "Natural Language :: English", - "Topic :: Multimedia :: Graphics :: Graphics Conversion" - ], - zip_safe=False) - \ No newline at end of file diff --git a/src/artist_pythonlib/__init__.py b/src/artist_pythonlib/__init__.py new file mode 100644 index 0000000..2aa4ad2 --- /dev/null +++ b/src/artist_pythonlib/__init__.py @@ -0,0 +1,12 @@ +# -*- coding: UTF-8 -*- +"""The aRTist Python library is intended to remote control and automate the radiographic simulator aRTist. + +.. include:: ./documentation.md +""" + +from .remote_connection import Junction +from .api import API +from .common_types import SAVEMODES, SOURCETYPES, PROJECTIONGEOMETRIES + + +__all__ = ["SAVEMODES", "SOURCETYPES", "PROJECTIONGEOMETRIES", "Junction", "API"] diff --git a/src/artist_pythonlib/api.py b/src/artist_pythonlib/api.py new file mode 100644 index 0000000..b3ecc79 --- /dev/null +++ b/src/artist_pythonlib/api.py @@ -0,0 +1,388 @@ +# Copyright 2023 Simon Wittl (Deggendorf Institute of Technology) +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +from __future__ import annotations + +import numpy as np + +from scipy.spatial.transform import Rotation +from pathlib import Path +import json + +from artist_pythonlib.geometries import projection_geometry, thd_projection_geometry +from artist_pythonlib.common_types import PROJECTIONGEOMETRIES, SAVEMODES +from artist_pythonlib.remote_connection import Junction, _rc + + +class API: + def __init__(self, remote_control: Junction = None) -> None: + if remote_control is None: + remote_control = _rc + self.rc = remote_control + + @staticmethod + def path_to_artist(path: Path) -> str: + return str(path.absolute()).replace("\\", "\\\\") + + def get_image(self) -> np.ndarray: + """Make a projection of the current scene. + + Returns: + np.ndarray: projection as ndarray. + """ + self.rc.send("set imgList [Engine::Go]") + self.rc.send("RemoteControl::SendImage [lindex $imgList 0]") + return self.rc.get_image() + + def save_image( + self, + save_path: Path, + save_mode: SAVEMODES = SAVEMODES.UINT16, + save_projection_geometry: PROJECTIONGEOMETRIES = PROJECTIONGEOMETRIES.NONE, + ): + """Save the current scene as projection. The projection geometry can be stored in a .json file. + + Args: + save_path (Path): Save path of the Projection + save_mode (SAVEMODES, optional): File type of saved projection. Defaults to SAVEMODES.UINT16. + save_projection_geometry (bool, optional): Projection geometry of the scene. Stem of save_path is used as path. Defaults to True. + """ + save_path = save_path.resolve() + if save_projection_geometry > 0: + if save_projection_geometry == PROJECTIONGEOMETRIES.THD: + geom = self.projection_geometry(save_projection_geometry) + + name = f'{save_path.stem}_{geom["header"]["uuid"]}' + save_path = save_path.parent / f"{name}.tif" + save_path_json = save_path.parent / f"{name}.json" + else: + save_path_json = save_path.parent / f"{save_path.stem}.json" + + with open(str(save_path_json), "w") as f: + json.dump(geom, f, indent=4) + + if save_mode == SAVEMODES.UINT8: + self._save_image_uint8(save_path) + elif save_mode == SAVEMODES.UINT16: + self._save_image_uint16(save_path) + elif save_mode == SAVEMODES.FLOAT_TIFF: + self._save_image_float_tiff(save_path) + elif save_mode == SAVEMODES.FLOAT_RAW: + self._save_image_float_raw(save_path) + elif save_mode == SAVEMODES.PNG: + self._save_image_png(save_path) + + def _save_image_uint16(self, save_path: Path): + """Saves the current scene as projection (.tif) and geometry (.json). + + Args: + save_path (Path): Save path of the projection. + """ + # self.rc.send('set imgList [Engine::Go]') + save_path_projection = str(save_path.absolute()).replace("\\", "\\\\") + self.rc.send( + f'set imgList [Engine::Go]; Image::SaveFloatTIFF [lindex $imgList 0] {save_path_projection} True; {r"foreach i $imgList {$i Delete}"}' + ) + + def _save_image_uint8(self, save_path: Path): + """Saves the current scene as projection (.tif) and geometry (.json). + + Args: + save_path (Path): Save path of the projection. + """ + # self.rc.send('set imgList [Engine::Go]') + save_path_projection = str(save_path.absolute()).replace("\\", "\\\\") + save_path_json = ( + save_path.parent / (save_path.stem + ".json") + ) # Image::SaveFile [lindex $imgList 0] [file join $env(HOME) Pictures/artistlib2.tif] true', + self.rc.send( + f'set imgList [Engine::Go]; Image::SaveFloatTIFF [lindex $imgList 0] {save_path_projection} True; {r"foreach i $imgList {$i Delete}"}' + ) + + with open(str(save_path_json), "w") as f: + json.dump(self.projection_geometry(), f, indent=4) + + def _save_image_float_tiff(self, save_path: Path): + """Saves the current scene as projection (.tiff) and geometry (.json). + + Args: + save_path (Path): Save path of the projection. + """ + # self.rc.send('set imgList [Engine::Go]') + save_path_projection = str(save_path.absolute()).replace("\\", "\\\\") + self.rc.send( + f'set imgList [Engine::Go]; Image::SaveFloatTIFF [lindex $imgList 0] {save_path_projection} True; {r"foreach i $imgList {$i Delete}"}' + ) + # self.rc.send('foreach i $imgList {$i Delete}') + + def _save_image_float_raw(self, save_path: Path): + """Saves the current scene as projection (.raw) and geometry (.json). + + Args: + save_path (Path): Save path of the projection. + """ + # self.rc.send('set imgList [Engine::Go]') + save_path_projection = str(save_path.absolute()).replace("\\", "\\\\") + save_path_json = ( + save_path.parent / (save_path.stem + ".json") + ) # Image::SaveFile [lindex $imgList 0] [file join $env(HOME) Pictures/artistlib2.tif] true', + self.rc.send( + f'set imgList [Engine::Go]; Image::SaveFloatTIFF [lindex $imgList 0] {save_path_projection} True; {r"foreach i $imgList {$i Delete}"}' + ) + + with open(str(save_path_json), "w") as f: + json.dump(self.projection_geometry(), f, indent=4) + + def _save_image_png(self, save_path: Path): + """Saves the current scene as projection (.png) and geometry (.json). + + Args: + save_path (Path): Save path of the projection. + """ + # self.rc.send('set imgList [Engine::Go]') + save_path_projection = str(save_path.absolute()).replace("\\", "\\\\") + self.rc.send( + f'set imgList [Engine::Go]; Image::SaveFloatTIFF [lindex $imgList 0] {save_path_projection} True; {r"foreach i $imgList {$i Delete}"}' + ) + + def translate( + self, id: int | str, x: float = 0.0, y: float = 0.0, z: float = 0.0 + ) -> None: + """Moves an object to an absolute position. All values in [mm]. + + Args: + id (int | str): ID of the Object. + x (float, optional): Absolute X position. Defaults to 0.0. + y (float, optional): Absolute Y position. Defaults to 0.0. + z (float, optional): Absolute Z position. Defaults to 0.0. + """ + self.rc.send( + f"::PartList::Invoke {str(id)} SetPosition {str(x)} {str(y)} {str(z)};" + ) + self.rc.send( + f"::PartList::Invoke {str(id)} SetRefPos {str(x)} {str(y)} {str(z)};" + ) + + def scale(self, id: int | str, x: float = 1.0) -> None: + """Moves an object to an absolute position. All values in [mm]. + + Args: + id (int | str): ID of the Object. + x (float, optional): Absolute X position. Defaults to 0.0. + y (float, optional): Absolute Y position. Defaults to 0.0. + z (float, optional): Absolute Z position. Defaults to 0.0. + """ + self.rc.send( + f"::PartList::Invoke {str(id)} SetScale {str(x)} {str(x)} {str(x)};" + ) + + def rotate( + self, id: int | str, alpha: float = 0.0, beta: float = 0.0, gamma: float = 0.0 + ) -> None: + """Rotates an object to an absolute position. All values in [°]. + + Args: + id (int | str): _description_ + alpha (float, optional): Absolute alpha rotation. Defaults to 0.0. + beta (float, optional): Absolute beta rotation. Defaults to 0.0. + gamma (float, optional): Absolute gamma rotation. Defaults to 0.0. + """ + position = self.get_position(id) + self.rc.send( + f"::PartList::Invoke {str(id)} SetRefPos {str(position[0])} {str(position[1])} {str(position[2])};" + ) + self.rc.send( + f"::PartList::Invoke {str(id)} SetOrientation {str(alpha)} {str(beta)} {str(gamma)};" + ) + + def rotate_from_rotation_matrix( + self, id: int | str, rotation_matrix: np.ndarray + ) -> None: + """Rotates an object to an absolute position. + + Args: + id (int | str): ID of the Object. + rotation_matrix (np.ndarray): Rotation matrix in world coordinate system. + """ + rotation = Rotation.from_matrix(rotation_matrix) + euler_scipy = rotation.as_euler("ZXY", degrees=True) + euler_scipy = [euler_scipy[1], euler_scipy[2], euler_scipy[0]] + self.rotate(id, *euler_scipy) + + def rotate_from_quat(self, id: int | str, qaurternion: np.ndarray) -> None: + """Rotates an object to an absolute position. + + Args: + id (int | str): ID of the Object. + qaurternion (np.ndarray): Quarternion in world coordinate system. + """ + self.rotate_from_rotation_matrix( + id, Rotation.from_quat(qaurternion).as_matrix() + ) + + def get_position(self, id: int | str) -> np.ndarray: + """Returns the current position of the object in [mm]. + + Args: + id (int | str): ID of the Object. + + Returns: + np.ndarray: position (x,y,z) in [mm]. + """ + result = self.rc.send(f"[::PartList::Get {id} Obj] GetPosition") + return np.float32(result[1:-1].split(" ")) + + def get_euler_angles(self, id: int | str) -> np.ndarray: + """Returns the current orientation of the object as euler angles in the ZXY convention. + + Args: + id (int | str): ID of the Object. + + + Returns: + np.ndarray: Euler angle in ZXY convention. + """ + result = self.rc.send(f"[::PartList::Get {id} Obj] GetOrientation") + return np.float32(result[1:-1].split(" ")) + + def get_rotation_matrix(self, id: int | str) -> np.ndarray: + euler_angles = self.get_euler_angles(id) + + R_x = Rotation.from_euler("x", euler_angles[0], degrees=True).as_matrix() + R_y = Rotation.from_euler("y", euler_angles[1], degrees=True).as_matrix() + R_z = Rotation.from_euler("z", euler_angles[2], degrees=True).as_matrix() + + # rotation = Rotation.from_euler('zxy', -euler_angles, degrees=True).as_matrix() + + rotation = R_z + rotation: np.ndarray = rotation.dot(R_x) + rotation = rotation.dot(R_y) + + # rotation = R_y + # rotation = rotation.dot(R_x) + # rotation = rotation.dot(R_z) + + return rotation + + def get_orientation(self, id) -> np.ndarray: + """Return the current orientation of the object as quaternion. + + Args: + id (int | str): ID of the Object. + + Returns: + np.ndarray: Quaternion of the object in the world coordinate system. + """ + rotation = Rotation.from_matrix(self.get_rotation_matrix(id)) + return rotation.as_quat() + + def projection_geometry( + self, mode: PROJECTIONGEOMETRIES = PROJECTIONGEOMETRIES.THD + ) -> dict: + """Returns the current projection geometry of the scene. All positions are in [mm]. + + Returns: + dict: Dictionary of the projection geometry. Keys are: 'focal_spot_position_mm', + 'focal_spot_orientation_matrix', 'detector_center_position_mm', + 'detector_center_orientation_matrix', 'detector_center_orientation_quat', + 'detector_count_px' and 'detector_resolution_mm' + """ + if mode == PROJECTIONGEOMETRIES.STANDARD: + return projection_geometry(self) + elif mode == PROJECTIONGEOMETRIES.THD: + return thd_projection_geometry(self) + + def get_detector_resolution(self) -> np.ndarray: + """Returns the current pixel pitch of the detector as array + + Returns: + np.ndarray: Pixel pitch of the detector (u, v). + """ + result = self.rc.send("::XDetector::GetResolution") + return np.array(np.float32(result.split(" "))) + + def get_detector_pixel_count(self) -> np.ndarray: + """Returns the current pixel count of the detector. + + Returns: + np.ndarray: Pixel count (u, v). + """ + result = self.rc.send("::XDetector::GetPixelSize") + return np.array(np.int32(result.split(" "))) + + def set_material(self, id: int | str, material: str): + """Changes the material of the object. + + Args: + id (int | str): ID of the Object. + material (str): Matiral as string. !!!Must be in the material database of artist!!! + """ + self.rc.send(f"::PartList::SetMaterial {material} {id}") + + def get_material(self, id: int | str): + """Returns the material of the object. + + Args: + id (int | str): ID of the Object. + """ + return_value = self.rc.send(f"::PartList::Get {id} Material") + return return_value + + def load_part( + self, load_path: Path, material: str = "Al", name: str = "Object" + ) -> int: + """Loads a mesh file into the artist scene. Returns the object id for further mainpulations. + + Args: + load_path (Path): Path object pointing to the mesh file. + material (str, optional): Material of the mesh file. Defaults to 'Al'. + name (str, optional): Displayed name in the aRTist GUI. Defaults to 'Object'. + + Returns: + int: Object ID for further Manipulations. + """ + return_value = self.rc.send( + f'set obj [::PartList::LoadPart "{self.path_to_artist(load_path)}" "{material}" "{name}"]' + ) + return int(return_value) + + def delete_part(self, id: int | str): + """Delets the object from the scene. + + Args: + id (int | str): ID of the Object. + """ + self.rc.send(f'::PartList::Delete "{id}"') + + def set_visibility(self, id: int | str, visible: bool = True): + """Sets the Object in/visiible. + + Args: + id (int | str): ID of the Object. + visible (bool, optional): Visible: True. Defaults to True. + """ + visible = "on" if visible else "off" + self.rc.send(f'[::PartList::Get {id} Obj] SetVisibility "{visible}"') + + def clear_scene(self): + """Clears all objects from the scene.""" + self.rc.send("::PartList::Clear") + + def load_project(self, project_file: Path): + if project_file.suffix != ".aRTist": + raise ValueError( + "Wrong File / Path. The *project_file* path must be a .aRTist File!" + ) + self.rc.send( + f'::XRayProject::LoadProject "{self.path_to_artist(project_file)}"' + ) diff --git a/src/artist_pythonlib/common_types.py b/src/artist_pythonlib/common_types.py new file mode 100644 index 0000000..c83a03a --- /dev/null +++ b/src/artist_pythonlib/common_types.py @@ -0,0 +1,34 @@ +# Copyright 2023 Simon Wittl (Deggendorf Institute of Technology) +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from enum import IntEnum + + +class SOURCETYPES(IntEnum): + MONOCHROMATIC = 0 + GENERAL = 1 + + +class SAVEMODES(IntEnum): + UINT8 = 0 + UINT16 = 1 + FLOAT_TIFF = 2 + FLOAT_RAW = 3 + PNG = 4 + + +class PROJECTIONGEOMETRIES(IntEnum): + NONE = 0 + STANDARD = 1 + THD = 2 diff --git a/src/artist_pythonlib/geometries/__init__.py b/src/artist_pythonlib/geometries/__init__.py new file mode 100644 index 0000000..890a2cb --- /dev/null +++ b/src/artist_pythonlib/geometries/__init__.py @@ -0,0 +1,4 @@ +from .standard_format import projection_geometry +from .thd_format import thd_projection_geometry + +__all__ = ["projection_geometry", "thd_projection_geometry"] diff --git a/src/artist_pythonlib/geometries/standard_format.py b/src/artist_pythonlib/geometries/standard_format.py new file mode 100644 index 0000000..144dcf5 --- /dev/null +++ b/src/artist_pythonlib/geometries/standard_format.py @@ -0,0 +1,39 @@ +from __future__ import annotations + +import numpy as np +from scipy.spatial.transform import Rotation + + +def projection_geometry(api) -> dict: + """Returns the current projection geometry of the scene. All positions are in [mm]. + + Returns: + dict: Dictionary of the projection geometry. Keys are: 'focal_spot_position_mm', + 'focal_spot_orientation_matrix', 'detector_center_position_mm', + 'detector_center_orientation_matrix', 'detector_center_orientation_quat', + 'detector_count_px' and 'detector_resolution_mm' + """ + source_position = np.array(api.get_position("S")) + source_orientation = np.array(api.get_rotation_matrix("S")) + detector_position = np.array(api.get_position("D")) + detector_orientation = np.array(api.get_rotation_matrix("D")) + + detector_resolution = api.get_detector_resolution() + detector_pixel_count = api.get_detector_pixel_count() + + data_dict = dict() + data_dict["focal_spot_position_mm"] = source_position.tolist() + data_dict["focal_spot_orientation_quat"] = ( + Rotation.from_matrix(source_orientation).as_quat().tolist() + ) + data_dict["detector_center_position_mm"] = detector_position.tolist() + data_dict["detector_center_orientation_quat"] = ( + Rotation.from_matrix(detector_orientation).as_quat().tolist() + ) + + data_dict["image_width_px"] = detector_pixel_count.tolist()[0] + data_dict["pixel_pitch_width_mm"] = detector_resolution.tolist()[0] + data_dict["image_height_px"] = detector_pixel_count.tolist()[1] + data_dict["pixel_pitch_height_mm"] = detector_resolution.tolist()[1] + + return data_dict diff --git a/src/artist_pythonlib/geometries/thd_format.py b/src/artist_pythonlib/geometries/thd_format.py new file mode 100644 index 0000000..0614591 --- /dev/null +++ b/src/artist_pythonlib/geometries/thd_format.py @@ -0,0 +1,64 @@ +import numpy as np +from scipy.spatial.transform import Rotation + +try: + from thd_json.header import generate_header +except ModuleNotFoundError: + from warnings import warn + + warn( + "The optional modules of `thd` is not installed. THD Json geometry is not available." + ) + + +def thd_projection_geometry(api) -> dict: + """Returns the current projection geometry of the scene. All positions are in [mm]. + + Returns: + dict: Dictionary of the projection geometry. Keys are: 'focal_spot_position_mm', + 'focal_spot_orientation_matrix', 'detector_center_position_mm', + 'detector_center_orientation_matrix', 'detector_center_orientation_quat', + 'detector_count_px' and 'detector_resolution_mm' + """ + source_position = np.array(api.get_position("S")) + source_orientation = np.array(api.get_rotation_matrix("S")) + detector_position = np.array(api.get_position("D")) + detector_orientation = np.array(api.get_rotation_matrix("D")) + + detector_resolution = api.get_detector_resolution() + detector_pixel_count = api.get_detector_pixel_count() + + data_dict = dict() + header_dict = dict() + projection_geometry = dict() + image = dict() + detector = dict() + + json_header = generate_header() + header_dict["uuid"] = json_header.uuid + header_dict["timestamp"] = json_header.timestamp + + projection_geometry["focal_spot_position_mm"] = source_position.tolist() + projection_geometry["focal_spot_orientation_quat"] = ( + Rotation.from_matrix(source_orientation).as_quat().tolist() + ) + projection_geometry["detector_center_position_mm"] = detector_position.tolist() + projection_geometry["detector_center_orientation_quat"] = ( + Rotation.from_matrix(detector_orientation).as_quat().tolist() + ) + + image["uuid"] = json_header.uuid + image["timestamp"] = json_header.timestamp + image["image_path"] = f"{json_header.uuid}.tif" + + detector["image_width_px"] = detector_pixel_count.tolist()[0] + detector["pixel_pitch_width_mm"] = detector_resolution.tolist()[0] + detector["image_height_px"] = detector_pixel_count.tolist()[1] + detector["pixel_pitch_height_mm"] = detector_resolution.tolist()[1] + + data_dict["projection_geometry"] = projection_geometry + data_dict["image"] = image + data_dict["detector"] = detector + data_dict["header"] = header_dict + + return data_dict diff --git a/src/artist_pythonlib/hardware/__init__.py b/src/artist_pythonlib/hardware/__init__.py new file mode 100644 index 0000000..e675328 --- /dev/null +++ b/src/artist_pythonlib/hardware/__init__.py @@ -0,0 +1,18 @@ +# Copyright 2023 Simon Wittl (Deggendorf Institute of Technology) +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from .xray_source import XraySource +from .xray_detector import XrayDetector + +__all__ = ["XraySource", "XrayDetector"] diff --git a/src/artist_pythonlib/hardware/base_hardware.py b/src/artist_pythonlib/hardware/base_hardware.py new file mode 100644 index 0000000..782cb37 --- /dev/null +++ b/src/artist_pythonlib/hardware/base_hardware.py @@ -0,0 +1,29 @@ +# Copyright 2023 Simon Wittl (Deggendorf Institute of Technology) +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +from __future__ import annotations + +from ..remote_connection import Junction, _rc +from ..api import API + + +class BaseHardware: + def __init__(self, remote_control: Junction | API = None) -> None: + if isinstance(remote_control, Junction): + self.rc = remote_control + elif isinstance(remote_control, API): + self.rc = remote_control.rc + elif remote_control is None: + self.rc = _rc + else: + raise ValueError("Wrong remote_control argument?") diff --git a/src/artist_pythonlib/hardware/xray_detector.py b/src/artist_pythonlib/hardware/xray_detector.py new file mode 100644 index 0000000..5e4a094 --- /dev/null +++ b/src/artist_pythonlib/hardware/xray_detector.py @@ -0,0 +1,73 @@ +# Copyright 2023 Simon Wittl (Deggendorf Institute of Technology) +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +from __future__ import annotations + +from artist_pythonlib.api import API +from artist_pythonlib.remote_connection import Junction +from .base_hardware import BaseHardware + +import numpy as np + + +class XrayDetector(BaseHardware): + def __init__(self, remote_control: Junction | API = None) -> None: + """XRay detector object. Needs a remote control connection. + + Args: + remote_control (Junction | API, optional): Remote control connection for the communication with artist. Defaults to None. + """ + super().__init__(remote_control) + + @property + def detector_resolution_mm(self) -> np.ndarray: + """Current detector resolution / pixel pitch in [mm]. + + Returns: + np.ndarray: Detector resolution (u, v) in [mm]. + """ + return_value = self.rc.send("::XDetector::GetResolution") + return_value = np.array(np.float32(return_value.split(" "))) + return return_value + + @detector_resolution_mm.setter + def detector_resolution_mm(self, detector_resolution_mm: np.ndarray) -> None: + self.rc.send(f"set ::Xsetup_private(DGdx) {detector_resolution_mm[0]}") + self.rc.send(f"set ::Xsetup_private(DGdy) {detector_resolution_mm[1]}") + + @property + def detector_count_px(self) -> np.ndarray: + """Current detector pixel count. + + Returns: + np.ndarray: Detector pixel count (u, v) in [n]. + """ + return_value = self.rc.send("::XDetector::GetPixelSize") + return_value = np.array(np.int32(return_value.split(" "))) + return return_value + + @detector_count_px.setter + def detector_count_px(self, detector_count_px: np.ndarray) -> None: + self.rc.send(f"set ::Xsetup(DetectorPixelX) {detector_count_px[0]}") + self.rc.send(f"set ::Xsetup(DetectorPixelY) {detector_count_px[1]}") + + @property + def flatfield_correction(self) -> bool: + """Faltfiled corrected? + + Returns: + bool: Return wheter the projection is flatfield corrected or not. + """ + return_value = self.rc.send("array get Xdetector FFCorrRun") + return_value = return_value.split(" ")[1] + return bool(return_value) diff --git a/src/artist_pythonlib/hardware/xray_source.py b/src/artist_pythonlib/hardware/xray_source.py new file mode 100644 index 0000000..f1f7878 --- /dev/null +++ b/src/artist_pythonlib/hardware/xray_source.py @@ -0,0 +1,117 @@ +# Copyright 2023 Simon Wittl (Deggendorf Institute of Technology) +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +from __future__ import annotations + + +from artist_pythonlib.api import API +from artist_pythonlib.remote_connection import Junction +from .base_hardware import BaseHardware + +from ..common_types import SOURCETYPES + + +class XraySource(BaseHardware): + def __init__(self, remote_control: Junction | API = None) -> None: + """Xray source objet. Needs a remote control connection. + + Args: + remote_control (Junction | API, optional): remote connection to communicate with aRTist. Defaults to None. + """ + super().__init__(remote_control) + + @property + def voltage_kv(self) -> float: + """Current voltage setting of the XRay source. + + Returns: + float: Voltage value in [kV]. + """ + return_value = self.rc.send("array get Xsource Voltage") + return_value = return_value.split(" ")[1] + return float(return_value) + + @voltage_kv.setter + def voltage_kv(self, voltage_kv: float) -> None: + self.rc.send(f"set ::Xsource(Voltage) {voltage_kv}") + self.rc.send("::XSource::ComputeSpectrum") + + @property + def exposure_ma(self) -> float: + """Current set exposure of the XRay source + + Returns: + float: Exposure in [µA]. + """ + return_value = self.rc.send("array get Xsource Exposure") + return_value = return_value.split(" ")[1] + return float(return_value) + + @exposure_ma.setter + def exposure_ma(self, exposure_ma: float) -> None: + self.rc.send(f"set ::Xsource(Exposure) {exposure_ma}") + + @property + def filter_material(self) -> str: + """Filter Material of the XRay source. + + Returns: + str: Filter material of the XRay source. + """ + return_value = self.rc.send("array get Xsource FilterMaterial") + return_value = return_value.split(" ")[1] + return str(return_value) + + @filter_material.setter + def filter_material(self, filter_material: float) -> None: + self.rc.send(f"set ::Xsource(FilterMaterial) {filter_material}") + self.rc.send("::XSource::ComputeSpectrum") + + @property + def filter_thickness_mm(self) -> float: + """Thickness of the filter in [mm]. + + Returns: + float: Filter thickness in [mm]. + """ + return_value = self.rc.send("array get Xsource FilterThickness") + return_value = return_value.split(" ")[1] + return float(return_value) + + @filter_thickness_mm.setter + def filter_thickness_mm(self, filter_thickness_mm: float) -> None: + self.rc.send(f"set ::Xsource(FilterThickness) {filter_thickness_mm}") + self.rc.send("::XSource::ComputeSpectrum") + + @property + def source_type(self) -> int: + """Source type of the XRay source. Types are Monocromatic or General. See SOURCETYPES. + + Returns: + int: Source type as integer. Use SOURCETYPES. + """ + return_value = self.rc.send("array get Xsource Tube") + return_value = return_value.split(" ")[1] + + if str(return_value).startswith("Mono"): + return SOURCETYPES.MONOCHROMATIC + elif str(return_value).startswith("General"): + return SOURCETYPES.GENERAL + + @source_type.setter + def source_type(self, source_type: SOURCETYPES) -> None: + if source_type == SOURCETYPES.MONOCHROMATIC: + self.rc.send("set ::Xsource(Tube) Mono") + elif source_type == SOURCETYPES.GENERAL: + self.rc.send("set ::Xsource(Tube) General") + self.rc.send("::XSource::ComputeSpectrum") diff --git a/src/artist_pythonlib/py.typed b/src/artist_pythonlib/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/src/artist_pythonlib/remote_connection.py b/src/artist_pythonlib/remote_connection.py new file mode 100644 index 0000000..a5163a8 --- /dev/null +++ b/src/artist_pythonlib/remote_connection.py @@ -0,0 +1,157 @@ +# Copyright 2023 Simon Wittl (Deggendorf Institute of Technology) +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +import numpy as np +import socket +import base64 +import pathlib +from PIL import Image + + +class Junction: + """Remote control of aRTist simulator (this is a test)""" + + def __init__(self, host="localhost", port=3658, bufferSize=1024, timeout=10): + self.host = host + self.port = port + self.bufferSize = bufferSize + self.timeout = timeout + self.error = 0 + self.progress = 0 + self.answer = {} + + self.connect() + + def connect(self): + try: + self.S = socket.socket() # Create socket (for TCP) + self.S.connect((self.host, self.port)) # Connect to aRTist + self.S.settimeout(self.timeout) + self.S.setblocking(True) + self.listen(0) + except ConnectionRefusedError: + print( + "The Connection to aRTist was refused. Is aRTist running and the remote connection enabled?" + ) + except Exception as e: + raise e + return self + + def send(self, command, msgType="RESULT"): + c = command + "\n" + self.S.send(c.encode()) + return self.listen(msgType=msgType) + + def listen(self, command_no=1, msgType="RESULT"): + answer = "" + stop = False + if command_no == 0: + self.S.settimeout(0.2) + while not stop: # and ("SUCCESS" not in total) and ("ERROR" not in total): # Solange server antwortet und nicht "SUCCESS" enthält + try: + msg = self.S.recv(self.bufferSize).decode() + except BaseException as e: + err = e.args[0] + if err == "timed out": + # print("Timeout\n") + answer += "RESULT Timeout\n" + # print(answer) + stop = True + continue + else: + if "SUCCESS" in msg: + answer += msg + stop = True + continue + elif "ERROR" in msg: + answer += msg + stop = True + # global error + self.error = self.error + 1 + continue + elif "PROGRESS" in msg: + try: + self.progress = float(msg.strip("PROGRESS ")) + except ValueError: + self.progress = 0 + continue + else: + if command_no == 0: + print(msg) + answer += msg + self.S.settimeout(self.timeout) + self.answer.update( + { + "SUCCESS": self.pick(answer, "SUCCESS"), + "RESULT": self.pick(answer, "RESULT"), + "SDTOUT": self.pick(answer, "STDOUT"), + "BASE64": self.pick(answer, "BASE64"), + "IMAGE": self.pick(answer, "IMAGE"), + "FILE": self.pick(answer, "FILE"), + } + ) + if msgType != "*": + answer = self.pick(answer, msgType) + return answer + + def pick(self, answer, res="RESULT"): + picked = "" + for a in answer.split("\n"): + if a.find(res) == 0: + picked += a[1 + len(res) :].strip("\r") + "\n" + if len(picked) == 0: + return res + " not found." + return picked + + def get_answer(self, key): + return self.answer[key] + + def save_image(self, imageName: str): + imageData = self.answer["BASE64"] + decodedData = base64.b64decode((imageData)) + imageHeader = self.answer["IMAGE"].split() + im = np.frombuffer(decodedData, np.double).reshape( + (int(imageHeader[1]), int(imageHeader[2])) + ) + Image.fromarray(im).save(imageName) + + def receive_file(self, fileName): + fileData = self.answer["BASE64"] + decodedFile = base64.b64decode((fileData)) + artistFile = open(fileName, "wb") + artistFile.write(decodedFile) + artistFile.close() + + def send_file(self, fileName): + outFile = open(fileName, "br") + fileBytes = outFile.read() + encBytes = base64.b64encode((fileBytes)) + encString = str(encBytes) + encString = encString.lstrip("b'").rstrip("'") + fileExtension = pathlib.Path(fileName).suffix + com = "::RemoteControl::ReceiveFile " + encString + " " + fileExtension + recAnswer = self.send(com, "RESULT") + return recAnswer + + def get_image(self) -> np.ndarray: + imageData = self.answer["BASE64"] + decodedData = base64.b64decode((imageData)) + imageHeader = self.answer["IMAGE"].split() + dtype = np.double + return np.frombuffer(decodedData, dtype).reshape( + (int(imageHeader[1]), int(imageHeader[2])) + ) + + +_rc = Junction() diff --git a/src/artist_pythonlib/trajectory/__init__.py b/src/artist_pythonlib/trajectory/__init__.py new file mode 100644 index 0000000..2d2d766 --- /dev/null +++ b/src/artist_pythonlib/trajectory/__init__.py @@ -0,0 +1,27 @@ +# Copyright 2023 Simon Wittl (Deggendorf Institute of Technology) +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from .ct_trajectories import ( + circular_trajectory, + look_at_orientation, + sphere_trajectory, + arbitary_circular_trajectory, +) + +__all__ = [ + "circular_trajectory", + "look_at_orientation", + "sphere_trajectory", + "arbitary_circular_trajectory", +] diff --git a/src/artist_pythonlib/trajectory/ct_trajectories.py b/src/artist_pythonlib/trajectory/ct_trajectories.py new file mode 100644 index 0000000..3b2d464 --- /dev/null +++ b/src/artist_pythonlib/trajectory/ct_trajectories.py @@ -0,0 +1,127 @@ +# Copyright 2023 Simon Wittl (Deggendorf Institute of Technology) +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +from __future__ import annotations + +import numpy as np +from scipy.spatial.transform import Rotation + + +def circular_trajectory( + fod_mm: float, fdd_mm: float, number_of_projections: int, opening_angle: float = 0.2 +) -> tuple[np.ndarray, np.ndarray, np.ndarray]: + if fod_mm > fdd_mm: + raise ValueError("fod > fdd.") + + rotation_angles = np.linspace( + 0.0, np.pi * (1.0 + opening_angle), number_of_projections, endpoint=False + ) + rotation_object = Rotation.from_euler("Y", rotation_angles, degrees=False) + + source_initial_position = np.array([0.0, 0.0, fod_mm]) + detector_initial_position = np.array([0.0, 0.0, fod_mm - fdd_mm]) + + source_positions = rotation_object.apply(source_initial_position) + detector_positions = rotation_object.apply(detector_initial_position) + + return source_positions, detector_positions, rotation_object.as_matrix() + + +def look_at_orientation( + source, detector, up_vector: np.ndarray = np.array([0.0, 0.0, 1.0]) +): + normal = source - detector + normal = normal / np.linalg.norm(normal) + + up_axis = int(np.argmax(up_vector)) + + line = np.cross(normal, up_vector) + col = np.cross(line, normal) + + if np.sign(col[up_axis]) != np.sign(up_vector[up_axis]): + col *= -1.0 + + line = np.cross(normal, col) + + rotation_matrix = np.eye(3) + rotation_matrix[:, 0] = line + rotation_matrix[:, 1] = col + rotation_matrix[:, 2] = normal + + if np.linalg.det(rotation_matrix) < 0.0: + rotation_matrix[:, np.argmax(up_vector)] *= -1.0 + + return rotation_matrix + + +def sphere_trajectory( + fod_mm: float, fdd_mm: float, number_of_projections: int +) -> tuple[np.ndarray, np.ndarray, np.ndarray]: + phi = (1.0 + np.sqrt(5.0)) / 2.0 + start = -(number_of_projections - 1.0) + end = number_of_projections - 1.0 + i = np.linspace(start, end, number_of_projections) + theta = np.divide(2.0 * i * np.pi, phi) + sphi = i / number_of_projections + cphi = ( + np.sqrt((number_of_projections + i) * (number_of_projections - i)) + / number_of_projections + ) + + point_array = np.zeros((number_of_projections, 3)) + + point_array[:, 0] = cphi * np.cos(theta) + point_array[:, 1] = cphi * np.sin(theta) + point_array[:, 2] = sphi + + source_positions = point_array * fod_mm + detector_positions = point_array * (fod_mm - fdd_mm) + orientation = np.array( + list(map(look_at_orientation, source_positions, detector_positions)) + ) + + return source_positions, detector_positions, orientation + + +def arbitary_circular_trajectory( + fod_mm: float, + fdd_mm: float, + number_of_projections: int, + transformation: np.ndarray = np.eye(4), + opening_angle: float = 0.2, +): + source_positions, detector_positions, orientation = circular_trajectory( + fod_mm, fdd_mm, number_of_projections, opening_angle + ) + + source_transformation_matrix = np.zeros((number_of_projections, 4, 4)) + source_transformation_matrix[:, 3, 3] = 1.0 + detector_transformation_matrix = source_transformation_matrix.copy() + + source_transformation_matrix[:, :3, 3] = source_positions + detector_transformation_matrix[:, :3, 3] = detector_positions + + source_transformation_matrix[:, :3, :3] = orientation + detector_transformation_matrix[:, :3, :3] = orientation + + transformation = np.expand_dims(transformation, 0) + source_transformation_matrix = transformation @ source_transformation_matrix + detector_transformation_matrix = transformation @ detector_transformation_matrix + + return ( + source_transformation_matrix[:, :3, 3].reshape((number_of_projections, 3)), + detector_transformation_matrix[:, :3, 3].reshape((number_of_projections, 3)), + detector_transformation_matrix[:, :3, :3].reshape( + (number_of_projections, 3, 3) + ), + ) diff --git a/src/artist_pythonlib/utility/__init__.py b/src/artist_pythonlib/utility/__init__.py new file mode 100644 index 0000000..d4b84c8 --- /dev/null +++ b/src/artist_pythonlib/utility/__init__.py @@ -0,0 +1,3 @@ +from .load_projection import load_projection, load_header + +__all__ = ["load_projection", "load_header"] diff --git a/src/artist_pythonlib/utility/load_projection.py b/src/artist_pythonlib/utility/load_projection.py new file mode 100644 index 0000000..0a46195 --- /dev/null +++ b/src/artist_pythonlib/utility/load_projection.py @@ -0,0 +1,27 @@ +from PIL import Image +import numpy as np +from pathlib import Path +import json +import time + + +def load_projection( + projection_path: Path, load_projection_geometry: bool = True +) -> tuple[np.ndarray, dict]: + try: + projection_array = np.array(Image.open(projection_path)) + except FileNotFoundError: + time.sleep(1) + projection_array = np.array(Image.open(projection_path)) + + if not load_projection_geometry: + return projection_array, None + else: + return projection_array, load_header(projection_path) + + +def load_header(projection_path) -> dict: + with open(str(projection_path.parent / f"{projection_path.stem}.json"), "r") as f: + projection_geometry = json.load(f) + + return projection_geometry diff --git a/uv.lock b/uv.lock new file mode 100644 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-# Version: 0.26 - -"""The Versioneer - like a rocketeer, but for versions. - -The Versioneer -============== - -* like a rocketeer, but for versions! -* https://github.com/python-versioneer/python-versioneer -* Brian Warner -* License: Public Domain (Unlicense) -* Compatible with: Python 3.7, 3.8, 3.9, 3.10 and pypy3 -* [![Latest Version][pypi-image]][pypi-url] -* [![Build Status][travis-image]][travis-url] - -This is a tool for managing a recorded version number in setuptools-based -python projects. The goal is to remove the tedious and error-prone "update -the embedded version string" step from your release process. Making a new -release should be as easy as recording a new tag in your version-control -system, and maybe making new tarballs. - - -## Quick Install - -Versioneer provides two installation modes. The "classic" vendored mode installs -a copy of versioneer into your repository. The experimental build-time dependency mode -is intended to allow you to skip this step and simplify the process of upgrading. - -### Vendored mode - -* `pip install versioneer` to somewhere in your $PATH -* add a `[tool.versioneer]` section to your `pyproject.toml or a - `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md)) -* run `versioneer install --vendor` in your source tree, commit the results -* verify version information with `python setup.py version` - -### Build-time dependency mode - -* `pip install versioneer` to somewhere in your $PATH -* add a `[tool.versioneer]` section to your `pyproject.toml or a - `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md)) -* add `versioneer` to the `requires` key of the `build-system` table in - `pyproject.toml`: - ```toml - [build-system] - requires = ["setuptools", "versioneer"] - build-backend = "setuptools.build_meta" - ``` -* run `versioneer install --no-vendor` in your source tree, commit the results -* verify version information with `python setup.py version` - -## Version Identifiers - -Source trees come from a variety of places: - -* a version-control system checkout (mostly used by developers) -* a nightly tarball, produced by build automation -* a snapshot tarball, produced by a web-based VCS browser, like github's - "tarball from tag" feature -* a release tarball, produced by "setup.py sdist", distributed through PyPI - -Within each source tree, the version identifier (either a string or a number, -this tool is format-agnostic) can come from a variety of places: - -* ask the VCS tool itself, e.g. "git describe" (for checkouts), which knows - about recent "tags" and an absolute revision-id -* the name of the directory into which the tarball was unpacked -* an expanded VCS keyword ($Id$, etc) -* a `_version.py` created by some earlier build step - -For released software, the version identifier is closely related to a VCS -tag. Some projects use tag names that include more than just the version -string (e.g. "myproject-1.2" instead of just "1.2"), in which case the tool -needs to strip the tag prefix to extract the version identifier. For -unreleased software (between tags), the version identifier should provide -enough information to help developers recreate the same tree, while also -giving them an idea of roughly how old the tree is (after version 1.2, before -version 1.3). Many VCS systems can report a description that captures this, -for example `git describe --tags --dirty --always` reports things like -"0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the -0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has -uncommitted changes). - -The version identifier is used for multiple purposes: - -* to allow the module to self-identify its version: `myproject.__version__` -* to choose a name and prefix for a 'setup.py sdist' tarball - -## Theory of Operation - -Versioneer works by adding a special `_version.py` file into your source -tree, where your `__init__.py` can import it. This `_version.py` knows how to -dynamically ask the VCS tool for version information at import time. - -`_version.py` also contains `$Revision$` markers, and the installation -process marks `_version.py` to have this marker rewritten with a tag name -during the `git archive` command. As a result, generated tarballs will -contain enough information to get the proper version. - -To allow `setup.py` to compute a version too, a `versioneer.py` is added to -the top level of your source tree, next to `setup.py` and the `setup.cfg` -that configures it. This overrides several distutils/setuptools commands to -compute the version when invoked, and changes `setup.py build` and `setup.py -sdist` to replace `_version.py` with a small static file that contains just -the generated version data. - -## Installation - -See [INSTALL.md](./INSTALL.md) for detailed installation instructions. - -## Version-String Flavors - -Code which uses Versioneer can learn about its version string at runtime by -importing `_version` from your main `__init__.py` file and running the -`get_versions()` function. From the "outside" (e.g. in `setup.py`), you can -import the top-level `versioneer.py` and run `get_versions()`. - -Both functions return a dictionary with different flavors of version -information: - -* `['version']`: A condensed version string, rendered using the selected - style. This is the most commonly used value for the project's version - string. The default "pep440" style yields strings like `0.11`, - `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section - below for alternative styles. - -* `['full-revisionid']`: detailed revision identifier. For Git, this is the - full SHA1 commit id, e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac". - -* `['date']`: Date and time of the latest `HEAD` commit. For Git, it is the - commit date in ISO 8601 format. This will be None if the date is not - available. - -* `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that - this is only accurate if run in a VCS checkout, otherwise it is likely to - be False or None - -* `['error']`: if the version string could not be computed, this will be set - to a string describing the problem, otherwise it will be None. It may be - useful to throw an exception in setup.py if this is set, to avoid e.g. - creating tarballs with a version string of "unknown". - -Some variants are more useful than others. Including `full-revisionid` in a -bug report should allow developers to reconstruct the exact code being tested -(or indicate the presence of local changes that should be shared with the -developers). `version` is suitable for display in an "about" box or a CLI -`--version` output: it can be easily compared against release notes and lists -of bugs fixed in various releases. - -The installer adds the following text to your `__init__.py` to place a basic -version in `YOURPROJECT.__version__`: - - from ._version import get_versions - __version__ = get_versions()['version'] - del get_versions - -## Styles - -The setup.cfg `style=` configuration controls how the VCS information is -rendered into a version string. - -The default style, "pep440", produces a PEP440-compliant string, equal to the -un-prefixed tag name for actual releases, and containing an additional "local -version" section with more detail for in-between builds. For Git, this is -TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags ---dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the -tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and -that this commit is two revisions ("+2") beyond the "0.11" tag. For released -software (exactly equal to a known tag), the identifier will only contain the -stripped tag, e.g. "0.11". - -Other styles are available. See [details.md](details.md) in the Versioneer -source tree for descriptions. - -## Debugging - -Versioneer tries to avoid fatal errors: if something goes wrong, it will tend -to return a version of "0+unknown". To investigate the problem, run `setup.py -version`, which will run the version-lookup code in a verbose mode, and will -display the full contents of `get_versions()` (including the `error` string, -which may help identify what went wrong). - -## Known Limitations - -Some situations are known to cause problems for Versioneer. This details the -most significant ones. More can be found on Github -[issues page](https://github.com/python-versioneer/python-versioneer/issues). - -### Subprojects - -Versioneer has limited support for source trees in which `setup.py` is not in -the root directory (e.g. `setup.py` and `.git/` are *not* siblings). The are -two common reasons why `setup.py` might not be in the root: - -* Source trees which contain multiple subprojects, such as - [Buildbot](https://github.com/buildbot/buildbot), which contains both - "master" and "slave" subprojects, each with their own `setup.py`, - `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI - distributions (and upload multiple independently-installable tarballs). -* Source trees whose main purpose is to contain a C library, but which also - provide bindings to Python (and perhaps other languages) in subdirectories. - -Versioneer will look for `.git` in parent directories, and most operations -should get the right version string. However `pip` and `setuptools` have bugs -and implementation details which frequently cause `pip install .` from a -subproject directory to fail to find a correct version string (so it usually -defaults to `0+unknown`). - -`pip install --editable .` should work correctly. `setup.py install` might -work too. - -Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in -some later version. - -[Bug #38](https://github.com/python-versioneer/python-versioneer/issues/38) is tracking -this issue. The discussion in -[PR #61](https://github.com/python-versioneer/python-versioneer/pull/61) describes the -issue from the Versioneer side in more detail. -[pip PR#3176](https://github.com/pypa/pip/pull/3176) and -[pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve -pip to let Versioneer work correctly. - -Versioneer-0.16 and earlier only looked for a `.git` directory next to the -`setup.cfg`, so subprojects were completely unsupported with those releases. - -### Editable installs with setuptools <= 18.5 - -`setup.py develop` and `pip install --editable .` allow you to install a -project into a virtualenv once, then continue editing the source code (and -test) without re-installing after every change. - -"Entry-point scripts" (`setup(entry_points={"console_scripts": ..})`) are a -convenient way to specify executable scripts that should be installed along -with the python package. - -These both work as expected when using modern setuptools. When using -setuptools-18.5 or earlier, however, certain operations will cause -`pkg_resources.DistributionNotFound` errors when running the entrypoint -script, which must be resolved by re-installing the package. This happens -when the install happens with one version, then the egg_info data is -regenerated while a different version is checked out. Many setup.py commands -cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into -a different virtualenv), so this can be surprising. - -[Bug #83](https://github.com/python-versioneer/python-versioneer/issues/83) describes -this one, but upgrading to a newer version of setuptools should probably -resolve it. - - -## Updating Versioneer - -To upgrade your project to a new release of Versioneer, do the following: - -* install the new Versioneer (`pip install -U versioneer` or equivalent) -* edit `setup.cfg` and `pyproject.toml`, if necessary, - to include any new configuration settings indicated by the release notes. - See [UPGRADING](./UPGRADING.md) for details. -* re-run `versioneer install --[no-]vendor` in your source tree, to replace - `SRC/_version.py` -* commit any changed files - -## Future Directions - -This tool is designed to make it easily extended to other version-control -systems: all VCS-specific components are in separate directories like -src/git/ . The top-level `versioneer.py` script is assembled from these -components by running make-versioneer.py . In the future, make-versioneer.py -will take a VCS name as an argument, and will construct a version of -`versioneer.py` that is specific to the given VCS. It might also take the -configuration arguments that are currently provided manually during -installation by editing setup.py . Alternatively, it might go the other -direction and include code from all supported VCS systems, reducing the -number of intermediate scripts. - -## Similar projects - -* [setuptools_scm](https://github.com/pypa/setuptools_scm/) - a non-vendored build-time - dependency -* [minver](https://github.com/jbweston/miniver) - a lightweight reimplementation of - versioneer -* [versioningit](https://github.com/jwodder/versioningit) - a PEP 518-based setuptools - plugin - -## License - -To make Versioneer easier to embed, all its code is dedicated to the public -domain. The `_version.py` that it creates is also in the public domain. -Specifically, both are released under the Creative Commons "Public Domain -Dedication" license (CC0-1.0), as described in -https://creativecommons.org/publicdomain/zero/1.0/ . - -[pypi-image]: https://img.shields.io/pypi/v/versioneer.svg -[pypi-url]: https://pypi.python.org/pypi/versioneer/ -[travis-image]: -https://img.shields.io/travis/com/python-versioneer/python-versioneer.svg -[travis-url]: https://travis-ci.com/github/python-versioneer/python-versioneer - -""" -# pylint:disable=invalid-name,import-outside-toplevel,missing-function-docstring -# pylint:disable=missing-class-docstring,too-many-branches,too-many-statements -# pylint:disable=raise-missing-from,too-many-lines,too-many-locals,import-error -# pylint:disable=too-few-public-methods,redefined-outer-name,consider-using-with -# pylint:disable=attribute-defined-outside-init,too-many-arguments - -import configparser -import errno -import json -import os -import re -import subprocess -import sys -from pathlib import Path -from typing import Callable, Dict -import functools -try: - import tomli - have_tomli = True -except ImportError: - have_tomli = False - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_root(): - """Get the project root directory. - - We require that all commands are run from the project root, i.e. the - directory that contains setup.py, setup.cfg, and versioneer.py . - """ - root = os.path.realpath(os.path.abspath(os.getcwd())) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - # allow 'python path/to/setup.py COMMAND' - root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0]))) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - err = ("Versioneer was unable to run the project root directory. " - "Versioneer requires setup.py to be executed from " - "its immediate directory (like 'python setup.py COMMAND'), " - "or in a way that lets it use sys.argv[0] to find the root " - "(like 'python path/to/setup.py COMMAND').") - raise VersioneerBadRootError(err) - try: - # Certain runtime workflows (setup.py install/develop in a setuptools - # tree) execute all dependencies in a single python process, so - # "versioneer" may be imported multiple times, and python's shared - # module-import table will cache the first one. So we can't use - # os.path.dirname(__file__), as that will find whichever - # versioneer.py was first imported, even in later projects. - my_path = os.path.realpath(os.path.abspath(__file__)) - me_dir = os.path.normcase(os.path.splitext(my_path)[0]) - vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0]) - if me_dir != vsr_dir and "VERSIONEER_PEP518" not in globals(): - print("Warning: build in %s is using versioneer.py from %s" - % (os.path.dirname(my_path), versioneer_py)) - except NameError: - pass - return root - - -def get_config_from_root(root): - """Read the project setup.cfg file to determine Versioneer config.""" - # This might raise OSError (if setup.cfg is missing), or - # configparser.NoSectionError (if it lacks a [versioneer] section), or - # configparser.NoOptionError (if it lacks "VCS="). See the docstring at - # the top of versioneer.py for instructions on writing your setup.cfg . - root = Path(root) - pyproject_toml = root / "pyproject.toml" - setup_cfg = root / "setup.cfg" - section = None - if pyproject_toml.exists() and have_tomli: - try: - with open(pyproject_toml, 'rb') as fobj: - pp = tomli.load(fobj) - section = pp['tool']['versioneer'] - except (tomli.TOMLDecodeError, KeyError): - pass - if not section: - parser = configparser.ConfigParser() - with open(setup_cfg) as cfg_file: - parser.read_file(cfg_file) - parser.get("versioneer", "VCS") # raise error if missing - - section = parser["versioneer"] - - cfg = VersioneerConfig() - cfg.VCS = section['VCS'] - cfg.style = section.get("style", "") - cfg.versionfile_source = section.get("versionfile_source") - cfg.versionfile_build = section.get("versionfile_build") - cfg.tag_prefix = section.get("tag_prefix") - if cfg.tag_prefix in ("''", '""', None): - cfg.tag_prefix = "" - cfg.parentdir_prefix = section.get("parentdir_prefix") - cfg.verbose = section.get("verbose") - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -# these dictionaries contain VCS-specific tools -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs, method): # decorator - """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - HANDLERS.setdefault(vcs, {})[method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen([command] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None), **popen_kwargs) - break - except OSError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, process.returncode - return stdout, process.returncode - - -LONG_VERSION_PY['git'] = r''' -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. -# Generated by versioneer-0.26 -# https://github.com/python-versioneer/python-versioneer - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys -from typing import Callable, Dict -import functools - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s" - git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s" - git_date = "%(DOLLAR)sFormat:%%ci%(DOLLAR)s" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "%(STYLE)s" - cfg.tag_prefix = "%(TAG_PREFIX)s" - cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s" - cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs, method): # decorator - """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen([command] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None), **popen_kwargs) - break - except OSError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %%s" %% dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %%s" %% (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %%s (error)" %% dispcmd) - print("stdout was %%s" %% stdout) - return None, process.returncode - return stdout, process.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %%s but none started with prefix %%s" %% - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %%d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r'\d', r)} - if verbose: - print("discarding '%%s', no digits" %% ",".join(refs - tags)) - if verbose: - print("likely tags: %%s" %% ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r'\d', r): - continue - if verbose: - print("picking %%s" %% r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %%s not under git control" %% root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner(GITS, [ - "describe", "--tags", "--dirty", "--always", "--long", - "--match", f"{tag_prefix}[[:digit:]]*" - ], cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], - cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%%s'" - %% describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%%s' doesn't start with prefix '%%s'" - print(fmt %% (full_tag, tag_prefix)) - pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'" - %% (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces): - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver): - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces): - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%%d.dev%%d" %% (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%%d" %% (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%%d" %% pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%%s'" %% style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for _ in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} -''' - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r'\d', r)} - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r'\d', r): - continue - if verbose: - print("picking %s" % r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner(GITS, [ - "describe", "--tags", "--dirty", "--always", "--long", - "--match", f"{tag_prefix}[[:digit:]]*" - ], cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], - cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%s'" - % describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = ("tag '%s' doesn't start with prefix '%s'" - % (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def do_vcs_install(versionfile_source, ipy): - """Git-specific installation logic for Versioneer. - - For Git, this means creating/changing .gitattributes to mark _version.py - for export-subst keyword substitution. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - files = [versionfile_source] - if ipy: - files.append(ipy) - if "VERSIONEER_PEP518" not in globals(): - try: - my_path = __file__ - if my_path.endswith(".pyc") or my_path.endswith(".pyo"): - my_path = os.path.splitext(my_path)[0] + ".py" - versioneer_file = os.path.relpath(my_path) - except NameError: - versioneer_file = "versioneer.py" - files.append(versioneer_file) - present = False - try: - with open(".gitattributes", "r") as fobj: - for line in fobj: - if line.strip().startswith(versionfile_source): - if "export-subst" in line.strip().split()[1:]: - present = True - break - except OSError: - pass - if not present: - with open(".gitattributes", "a+") as fobj: - fobj.write(f"{versionfile_source} export-subst\n") - files.append(".gitattributes") - run_command(GITS, ["add", "--"] + files) - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %s but none started with prefix %s" % - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -SHORT_VERSION_PY = """ -# This file was generated by 'versioneer.py' (0.26) from -# revision-control system data, or from the parent directory name of an -# unpacked source archive. Distribution tarballs contain a pre-generated copy -# of this file. - -import json - -version_json = ''' -%s -''' # END VERSION_JSON - - -def get_versions(): - return json.loads(version_json) -""" - - -def versions_from_file(filename): - """Try to determine the version from _version.py if present.""" - try: - with open(filename) as f: - contents = f.read() - except OSError: - raise NotThisMethod("unable to read _version.py") - mo = re.search(r"version_json = '''\n(.*)''' # END VERSION_JSON", - contents, re.M | re.S) - if not mo: - mo = re.search(r"version_json = '''\r\n(.*)''' # END VERSION_JSON", - contents, re.M | re.S) - if not mo: - raise NotThisMethod("no version_json in _version.py") - return json.loads(mo.group(1)) - - -def write_to_version_file(filename, versions): - """Write the given version number to the given _version.py file.""" - os.unlink(filename) - contents = json.dumps(versions, sort_keys=True, - indent=1, separators=(",", ": ")) - with open(filename, "w") as f: - f.write(SHORT_VERSION_PY % contents) - - print("set %s to '%s'" % (filename, versions["version"])) - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces): - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver): - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces): - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%d" % (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -class VersioneerBadRootError(Exception): - """The project root directory is unknown or missing key files.""" - - -def get_versions(verbose=False): - """Get the project version from whatever source is available. - - Returns dict with two keys: 'version' and 'full'. - """ - if "versioneer" in sys.modules: - # see the discussion in cmdclass.py:get_cmdclass() - del sys.modules["versioneer"] - - root = get_root() - cfg = get_config_from_root(root) - - assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg" - handlers = HANDLERS.get(cfg.VCS) - assert handlers, "unrecognized VCS '%s'" % cfg.VCS - verbose = verbose or cfg.verbose - assert cfg.versionfile_source is not None, \ - "please set versioneer.versionfile_source" - assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix" - - versionfile_abs = os.path.join(root, cfg.versionfile_source) - - # extract version from first of: _version.py, VCS command (e.g. 'git - # describe'), parentdir. This is meant to work for developers using a - # source checkout, for users of a tarball created by 'setup.py sdist', - # and for users of a tarball/zipball created by 'git archive' or github's - # download-from-tag feature or the equivalent in other VCSes. - - get_keywords_f = handlers.get("get_keywords") - from_keywords_f = handlers.get("keywords") - if get_keywords_f and from_keywords_f: - try: - keywords = get_keywords_f(versionfile_abs) - ver = from_keywords_f(keywords, cfg.tag_prefix, verbose) - if verbose: - print("got version from expanded keyword %s" % ver) - return ver - except NotThisMethod: - pass - - try: - ver = versions_from_file(versionfile_abs) - if verbose: - print("got version from file %s %s" % (versionfile_abs, ver)) - return ver - except NotThisMethod: - pass - - from_vcs_f = handlers.get("pieces_from_vcs") - if from_vcs_f: - try: - pieces = from_vcs_f(cfg.tag_prefix, root, verbose) - ver = render(pieces, cfg.style) - if verbose: - print("got version from VCS %s" % ver) - return ver - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - if verbose: - print("got version from parentdir %s" % ver) - return ver - except NotThisMethod: - pass - - if verbose: - print("unable to compute version") - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, "error": "unable to compute version", - "date": None} - - -def get_version(): - """Get the short version string for this project.""" - return get_versions()["version"] - - -def get_cmdclass(cmdclass=None): - """Get the custom setuptools subclasses used by Versioneer. - - If the package uses a different cmdclass (e.g. one from numpy), it - should be provide as an argument. - """ - if "versioneer" in sys.modules: - del sys.modules["versioneer"] - # this fixes the "python setup.py develop" case (also 'install' and - # 'easy_install .'), in which subdependencies of the main project are - # built (using setup.py bdist_egg) in the same python process. Assume - # a main project A and a dependency B, which use different versions - # of Versioneer. A's setup.py imports A's Versioneer, leaving it in - # sys.modules by the time B's setup.py is executed, causing B to run - # with the wrong versioneer. Setuptools wraps the sub-dep builds in a - # sandbox that restores sys.modules to it's pre-build state, so the - # parent is protected against the child's "import versioneer". By - # removing ourselves from sys.modules here, before the child build - # happens, we protect the child from the parent's versioneer too. - # Also see https://github.com/python-versioneer/python-versioneer/issues/52 - - cmds = {} if cmdclass is None else cmdclass.copy() - - # we add "version" to setuptools - from setuptools import Command - - class cmd_version(Command): - description = "report generated version string" - user_options = [] - boolean_options = [] - - def initialize_options(self): - pass - - def finalize_options(self): - pass - - def run(self): - vers = get_versions(verbose=True) - print("Version: %s" % vers["version"]) - print(" full-revisionid: %s" % vers.get("full-revisionid")) - print(" dirty: %s" % vers.get("dirty")) - print(" date: %s" % vers.get("date")) - if vers["error"]: - print(" error: %s" % vers["error"]) - cmds["version"] = cmd_version - - # we override "build_py" in setuptools - # - # most invocation pathways end up running build_py: - # distutils/build -> build_py - # distutils/install -> distutils/build ->.. - # setuptools/bdist_wheel -> distutils/install ->.. - # setuptools/bdist_egg -> distutils/install_lib -> build_py - # setuptools/install -> bdist_egg ->.. - # setuptools/develop -> ? - # pip install: - # copies source tree to a tempdir before running egg_info/etc - # if .git isn't copied too, 'git describe' will fail - # then does setup.py bdist_wheel, or sometimes setup.py install - # setup.py egg_info -> ? - - # pip install -e . and setuptool/editable_wheel will invoke build_py - # but the build_py command is not expected to copy any files. - - # we override different "build_py" commands for both environments - if 'build_py' in cmds: - _build_py = cmds['build_py'] - else: - from setuptools.command.build_py import build_py as _build_py - - class cmd_build_py(_build_py): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_py.run(self) - if getattr(self, "editable_mode", False): - # During editable installs `.py` and data files are - # not copied to build_lib - return - # now locate _version.py in the new build/ directory and replace - # it with an updated value - if cfg.versionfile_build: - target_versionfile = os.path.join(self.build_lib, - cfg.versionfile_build) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - cmds["build_py"] = cmd_build_py - - if 'build_ext' in cmds: - _build_ext = cmds['build_ext'] - else: - from setuptools.command.build_ext import build_ext as _build_ext - - class cmd_build_ext(_build_ext): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_ext.run(self) - if self.inplace: - # build_ext --inplace will only build extensions in - # build/lib<..> dir with no _version.py to write to. - # As in place builds will already have a _version.py - # in the module dir, we do not need to write one. - return - # now locate _version.py in the new build/ directory and replace - # it with an updated value - target_versionfile = os.path.join(self.build_lib, - cfg.versionfile_build) - if not os.path.exists(target_versionfile): - print(f"Warning: {target_versionfile} does not exist, skipping " - "version update. This can happen if you are running build_ext " - "without first running build_py.") - return - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - cmds["build_ext"] = cmd_build_ext - - if "cx_Freeze" in sys.modules: # cx_freeze enabled? - from cx_Freeze.dist import build_exe as _build_exe - # nczeczulin reports that py2exe won't like the pep440-style string - # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g. - # setup(console=[{ - # "version": versioneer.get_version().split("+", 1)[0], # FILEVERSION - # "product_version": versioneer.get_version(), - # ... - - class cmd_build_exe(_build_exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _build_exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % - {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - cmds["build_exe"] = cmd_build_exe - del cmds["build_py"] - - if 'py2exe' in sys.modules: # py2exe enabled? - try: - from py2exe.setuptools_buildexe import py2exe as _py2exe - except ImportError: - from py2exe.distutils_buildexe import py2exe as _py2exe - - class cmd_py2exe(_py2exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _py2exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % - {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - cmds["py2exe"] = cmd_py2exe - - # sdist farms its file list building out to egg_info - if 'egg_info' in cmds: - _sdist = cmds['egg_info'] - else: - from setuptools.command.egg_info import egg_info as _egg_info - - class cmd_egg_info(_egg_info): - def find_sources(self): - # egg_info.find_sources builds the manifest list and writes it - # in one shot - super().find_sources() - - # Modify the filelist and normalize it - root = get_root() - cfg = get_config_from_root(root) - self.filelist.append('versioneer.py') - if cfg.versionfile_source: - # There are rare cases where versionfile_source might not be - # included by default, so we must be explicit - self.filelist.append(cfg.versionfile_source) - self.filelist.sort() - self.filelist.remove_duplicates() - - # The write method is hidden in the manifest_maker instance that - # generated the filelist and was thrown away - # We will instead replicate their final normalization (to unicode, - # and POSIX-style paths) - from setuptools import unicode_utils - normalized = [unicode_utils.filesys_decode(f).replace(os.sep, '/') - for f in self.filelist.files] - - manifest_filename = os.path.join(self.egg_info, 'SOURCES.txt') - with open(manifest_filename, 'w') as fobj: - fobj.write('\n'.join(normalized)) - - cmds['egg_info'] = cmd_egg_info - - # we override different "sdist" commands for both environments - if 'sdist' in cmds: - _sdist = cmds['sdist'] - else: - from setuptools.command.sdist import sdist as _sdist - - class cmd_sdist(_sdist): - def run(self): - versions = get_versions() - self._versioneer_generated_versions = versions - # unless we update this, the command will keep using the old - # version - self.distribution.metadata.version = versions["version"] - return _sdist.run(self) - - def make_release_tree(self, base_dir, files): - root = get_root() - cfg = get_config_from_root(root) - _sdist.make_release_tree(self, base_dir, files) - # now locate _version.py in the new base_dir directory - # (remembering that it may be a hardlink) and replace it with an - # updated value - target_versionfile = os.path.join(base_dir, cfg.versionfile_source) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, - self._versioneer_generated_versions) - cmds["sdist"] = cmd_sdist - - return cmds - - -CONFIG_ERROR = """ -setup.cfg is missing the necessary Versioneer configuration. You need -a section like: - - [versioneer] - VCS = git - style = pep440 - versionfile_source = src/myproject/_version.py - versionfile_build = myproject/_version.py - tag_prefix = - parentdir_prefix = myproject- - -You will also need to edit your setup.py to use the results: - - import versioneer - setup(version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), ...) - -Please read the docstring in ./versioneer.py for configuration instructions, -edit setup.cfg, and re-run the installer or 'python versioneer.py setup'. -""" - -SAMPLE_CONFIG = """ -# See the docstring in versioneer.py for instructions. Note that you must -# re-run 'versioneer.py setup' after changing this section, and commit the -# resulting files. - -[versioneer] -#VCS = git -#style = pep440 -#versionfile_source = -#versionfile_build = -#tag_prefix = -#parentdir_prefix = - -""" - -OLD_SNIPPET = """ -from ._version import get_versions -__version__ = get_versions()['version'] -del get_versions -""" - -INIT_PY_SNIPPET = """ -from . import {0} -__version__ = {0}.get_versions()['version'] -""" - - -def do_setup(): - """Do main VCS-independent setup function for installing Versioneer.""" - root = get_root() - try: - cfg = get_config_from_root(root) - except (OSError, configparser.NoSectionError, - configparser.NoOptionError) as e: - if isinstance(e, (OSError, configparser.NoSectionError)): - print("Adding sample versioneer config to setup.cfg", - file=sys.stderr) - with open(os.path.join(root, "setup.cfg"), "a") as f: - f.write(SAMPLE_CONFIG) - print(CONFIG_ERROR, file=sys.stderr) - return 1 - - print(" creating %s" % cfg.versionfile_source) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - - ipy = os.path.join(os.path.dirname(cfg.versionfile_source), - "__init__.py") - if os.path.exists(ipy): - try: - with open(ipy, "r") as f: - old = f.read() - except OSError: - old = "" - module = os.path.splitext(os.path.basename(cfg.versionfile_source))[0] - snippet = INIT_PY_SNIPPET.format(module) - if OLD_SNIPPET in old: - print(" replacing boilerplate in %s" % ipy) - with open(ipy, "w") as f: - f.write(old.replace(OLD_SNIPPET, snippet)) - elif snippet not in old: - print(" appending to %s" % ipy) - with open(ipy, "a") as f: - f.write(snippet) - else: - print(" %s unmodified" % ipy) - else: - print(" %s doesn't exist, ok" % ipy) - ipy = None - - # Make VCS-specific changes. For git, this means creating/changing - # .gitattributes to mark _version.py for export-subst keyword - # substitution. - do_vcs_install(cfg.versionfile_source, ipy) - return 0 - - -def scan_setup_py(): - """Validate the contents of setup.py against Versioneer's expectations.""" - found = set() - setters = False - errors = 0 - with open("setup.py", "r") as f: - for line in f.readlines(): - if "import versioneer" in line: - found.add("import") - if "versioneer.get_cmdclass()" in line: - found.add("cmdclass") - if "versioneer.get_version()" in line: - found.add("get_version") - if "versioneer.VCS" in line: - setters = True - if "versioneer.versionfile_source" in line: - setters = True - if len(found) != 3: - print("") - print("Your setup.py appears to be missing some important items") - print("(but I might be wrong). Please make sure it has something") - print("roughly like the following:") - print("") - print(" import versioneer") - print(" setup( version=versioneer.get_version(),") - print(" cmdclass=versioneer.get_cmdclass(), ...)") - print("") - errors += 1 - if setters: - print("You should remove lines like 'versioneer.VCS = ' and") - print("'versioneer.versionfile_source = ' . This configuration") - print("now lives in setup.cfg, and should be removed from setup.py") - print("") - errors += 1 - return errors - - -def setup_command(): - """Set up Versioneer and exit with appropriate error code.""" - errors = do_setup() - errors += scan_setup_py() - sys.exit(1 if errors else 0) - - -if __name__ == "__main__": - cmd = sys.argv[1] - if cmd == "setup": - setup_command()