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Support for newer version #8

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7616913
Update sifreader.py
mryzmo Feb 25, 2020
a9ca94c
Merge pull request #1 from mryzmo/mryzmo-patch-1
mryzmo Feb 25, 2020
57cc32e
Update sifreader.py
mryzmo Feb 25, 2020
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49 changes: 20 additions & 29 deletions sifreader/sifreader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import os
import time
import numpy as np
from scanf import scanf


class SIFFile(object):
Expand Down Expand Up @@ -71,14 +72,17 @@ def __repr__(self):

res = super().__repr__() + '\n' + res
return res

def _read_header(self, filepath):
def _read_header(self, filepath, verbose=False):
f = open(filepath, 'rb')
headerlen = 32
headerlen = 50
spool = 0
i = 0
pxnumline=0
while i < headerlen + spool:
line = f.readline().strip()
if verbose:
print(str(i)+':'+str(f.tell())+': '+str(line))
if i == 0:
if line != b'Andor Technology Multi-Channel File':
f.close()
Expand All @@ -102,29 +106,15 @@ def _read_header(self, filepath):
tokens = line.split()
if len(tokens) >= 1 and tokens[0] == 'Spooled':
spool = 1
if i == 9:
wavelength_info = line.split()
self.center_wavelength = float(wavelength_info[3])
self.grating = float(wavelength_info[6])
self.grating_blaze = float(wavelength_info[7])
if i == 19:
self.wavelength_coefficients = [float(num) for num in line.split()][::-1]
if 7 < i < headerlen - 12:
if len(line) == 17 and line[0:6] == b'65539 ':
# and line[7] == b'x01' and line[8] == b'x20' \
# and line[9] == b'x00':
headerlen = i + 12
if i == headerlen - 2:
if line[:12] == b'Pixel number':
line = line[12:]
tokens = line.split()
if len(tokens) < 6:
raise Exception('Not able to read stacksize.')
elif line.startswith(b'Pixel number') and pxnumline==0:
pxnumline=i
elif i == pxnumline+2 and pxnumline>0:
tokens=scanf('Pixel number%d %d %d %d %d %d %d %d %d', s=str(line), collapseWhitespace=False)
self.yres = int(tokens[2])
self.xres = int(tokens[3])
self.stacksize = int(tokens[5])
elif i == headerlen - 1:
tokens = line.split()
elif i == pxnumline+3 and pxnumline>0:
tokens = scanf('%d %d %d %d %d %d %d', s=str(line), collapseWhitespace=False)
if len(tokens) < 7:
raise Exception("Not able to read Image dimensions.")
self.left = int(tokens[1])
Expand All @@ -133,6 +123,13 @@ def _read_header(self, filepath):
self.bottom = int(tokens[4])
self.xbin = int(tokens[5])
self.ybin = int(tokens[6])
elif i>=pxnumline+4 and pxnumline > 0:# and str(line)==b'0':
#'End of header, looking for start of data!'
for i in range(self.stacksize):
f.readline()
#'Header end: '+str(f.tell()))
self.m_offset = f.tell()
break;
i += 1

f.close()
Expand All @@ -144,12 +141,6 @@ def _read_header(self, filepath):
mod = height % self.ybin
self.height = int((height - mod) / self.xbin)

self.filesize = os.path.getsize(filepath)
self.datasize = self.width * self.height * 4 * self.stacksize
self.m_offset = self.filesize - self.datasize - 8

self.x_axis = np.polyval(self.wavelength_coefficients, np.arange(self.left, self.right + 1))

def read_block(self, num=0):
"""
Returns a specific block (i.e. frame) in the .sif file as a numpy array.
Expand Down