Comment bugfix

.gitignore

@@ -5,3 +5,5 @@ __pycache__
 .DS_Store
 *.egg-info/
 .idea
+test*
+.env*

brpylib/brMiscFxns.py

@@ -28,17 +28,19 @@
     pass
 
 
-def openfilecheck(open_mode, file_name="", file_ext="", file_type=""):
+def openfilecheck(open_mode, file_name="", file_ext="", file_type="", verbose=True, interactive=True):
     """
     :param open_mode: {str} method to open the file (e.g., 'rb' for binary read only)
     :param file_name: [optional] {str} full path of file to open
     :param file_ext:  [optional] {str} file extension (e.g., '.nev')
     :param file_type: [optional] {str} file type for use when browsing for file (e.g., 'Blackrock NEV Files')
+    :param verbose: [optional] {bool} whether or not to print status information
+    :param interactive: [optional] {bool} will only try to prompt user for a file if True, otherwise allow failure
     :return: {file} opened file
     """
 
     while True:
-        if not file_name:  # no file name passed
+        if interactive and not file_name:  # no file name passed
             if not HAS_QT:
                 raise ModuleNotFoundError(
                     "Qt required for file dialog. Install PySide + qtpy or provide file_name."
@@ -75,19 +77,23 @@ def openfilecheck(open_mode, file_name="", file_ext="", file_type=""):
                     test_extension = file_ext
 
                 if fext[0 : len(test_extension)] != test_extension:
-                    file_name = ""
-                    print(
-                        "\n*** File given is not a "
-                        + file_ext
-                        + " file, try again ***\n"
-                    )
-                    continue
+                    if interactive:
+                        file_name = ""
+                        print(
+                            "\n*** File given is not a "
+                            + file_ext
+                            + " file, try again ***\n"
+                        )
+                        continue
+                    else:
+                        break
             break
         else:
             file_name = ""
             print("\n*** File given does exist, try again ***\n")
+    if verbose:
+        print("\n" + file_name.split("/")[-1] + " opened")
 
-    print("\n" + file_name.split("/")[-1] + " opened")
     return open(file_name, open_mode)
 
 

brpylib/brpylib.py

@@ -512,7 +512,7 @@ class NevFile:
     basic header information.
     """
 
-    def __init__(self, datafile=""):
+    def __init__(self, datafile="", verbose=True, interactive=True):
         self.datafile = datafile
         self.basic_header = {}
         self.extended_headers = []
@@ -523,6 +523,8 @@ def __init__(self, datafile=""):
             file_name=self.datafile,
             file_ext=".nev",
             file_type="Blackrock NEV Files",
+            verbose=verbose,
+            interactive=interactive
         )
 
         # extract basic header information
@@ -732,16 +734,17 @@ def getdata(self, elec_ids="all", wave_read="read"):
 
             # extract only the "true" comments, distinct from ROI packets
             trueComments = np.setdiff1d(
-                list(range(0, len(commentPackets) - 1)), ROIPackets
-            )
+                list(range(0, len(commentPackets))), ROIPackets
+            ).astype(int)
             trueCommentsidx = np.asarray(commentPackets)[trueComments]
             textComments = comments[trueCommentsidx]
-            textComments[:, -1] = "$"
-            stringarray = textComments.tostring()
-            stringvector = stringarray.decode("latin-1")
-            stringvector = stringvector[0:-1]
-            validstrings = stringvector.replace("\x00", "")
-            commentsFinal = validstrings.split("$")
+            commentsFinal = []
+            for text in textComments:
+                stringarray = text.astype(str).tobytes()
+                stringvector = stringarray.decode("latin-1")
+                stringvector = stringvector[0:-1]
+                validstring = stringvector.replace("\x00", "")
+                commentsFinal.append(validstring)
 
             # Remove the ROI comments from the list
             subsetInds = list(
@@ -761,7 +764,7 @@ def getdata(self, elec_ids="all", wave_read="read"):
                 nmCommentsidx = np.asarray(commentPackets)[ROIPackets]
                 nmcomments = comments[nmCommentsidx]
                 nmcomments[:, -1] = ":"
-                nmstringarray = nmcomments.tostring()
+                nmstringarray = nmcomments.astype(str).tobytes()
                 nmstringvector = nmstringarray.decode("latin-1")
                 nmstringvector = nmstringvector[0:-1]
                 nmvalidstrings = nmstringvector.replace("\x00", "")
@@ -1020,7 +1023,7 @@ class NsxFile:
     basic header information.
     """
 
-    def __init__(self, datafile=""):
+    def __init__(self, datafile="", interactive=True, verbose=True):
 
         self.datafile = datafile
         self.basic_header = {}
@@ -1032,6 +1035,8 @@ def __init__(self, datafile=""):
             file_name=self.datafile,
             file_ext=".ns*",
             file_type="Blackrock NSx Files",
+            interactive=interactive,
+            verbose=verbose
         )
 
         # Determine File ID to determine if File Spec 2.1
@@ -1219,11 +1224,8 @@ def getdata(
                     # memmap moves the file pointer inconsistently depending on platform and numpy version
                     curr_loc = self.datafile.tell()
                     expected_loc = bod + num_data_pts * data_pt_size
-                    if curr_loc == bod:
-                        # It did not move the pointer at all. Move it manually.
-                        self.datafile.seek(expected_loc - bod, 1)
-                    elif curr_loc > expected_loc:
-                        # Moved it too far (probably to end of file); move manually from beginning to expected.
+                    if curr_loc != expected_loc:
+                        # memmap moved the cursor to an unexpected location, update it manually
                         self.datafile.seek(expected_loc, 0)
             else:
                 # 1 sample per packet. Reuse struct_arr.

build/lib/brpylib/__init__.py

@@ -0,0 +1 @@
+from .brpylib import NevFile, NsxFile, brpylib_ver

build/lib/brpylib/brMiscFxns.py

@@ -0,0 +1,106 @@
+"""
+Random functions that may be useful elsewhere (or necessary)
+current version: 1.2.0 --- 08/04/2016
+
+@author: Mitch Frankel - Blackrock Microsystems
+
+Version History:
+v1.0.0 - 07/05/2016 - initial release
+v1.1.0 - 07/12/2016 - minor editing changes to print statements and addition of version control
+v1.2.0 - 08/04/2016 - minor modifications to allow use of Python 2.6+
+"""
+from os import getcwd, path
+
+try:
+    from qtpy.QtWidgets import QApplication, QFileDialog
+
+    HAS_QT = True
+except ModuleNotFoundError:
+    HAS_QT = False
+
+# Version control
+brmiscfxns_ver = "1.2.0"
+
+# Patch for use with Python 2.6+
+try:
+    input = raw_input
+except NameError:
+    pass
+
+
+def openfilecheck(open_mode, file_name="", file_ext="", file_type="", verbose=True, interactive=True):
+    """
+    :param open_mode: {str} method to open the file (e.g., 'rb' for binary read only)
+    :param file_name: [optional] {str} full path of file to open
+    :param file_ext:  [optional] {str} file extension (e.g., '.nev')
+    :param file_type: [optional] {str} file type for use when browsing for file (e.g., 'Blackrock NEV Files')
+    :param verbose: [optional] {bool} whether or not to print status information
+    :param interactive: [optional] {bool} will only try to prompt user for a file if True, otherwise allow failure
+    :return: {file} opened file
+    """
+
+    while True:
+        if interactive and not file_name:  # no file name passed
+            if not HAS_QT:
+                raise ModuleNotFoundError(
+                    "Qt required for file dialog. Install PySide + qtpy or provide file_name."
+                )
+
+            # Ask user to specify a file path or browse
+            file_name = input(
+                "Enter complete " + file_ext + " file path or hit enter to browse: "
+            )
+
+            if not file_name:
+                if "app" not in locals():
+                    app = QApplication([])
+                if not file_ext:
+                    file_type = "All Files"
+                file_name = QFileDialog.getOpenFileName(
+                    QFileDialog(),
+                    "Select File",
+                    getcwd(),
+                    file_type + " (*" + file_ext + ")",
+                )
+                file_name = file_name[0]
+
+        # Ensure file exists (really needed for users type entering)
+        if path.isfile(file_name):
+            # Ensure given file matches file_ext
+            if file_ext:
+                _, fext = path.splitext(file_name)
+
+                # check for * in extension
+                if file_ext[-1] == "*":
+                    test_extension = file_ext[:-1]
+                else:
+                    test_extension = file_ext
+
+                if fext[0 : len(test_extension)] != test_extension:
+                    if interactive:
+                        file_name = ""
+                        print(
+                            "\n*** File given is not a "
+                            + file_ext
+                            + " file, try again ***\n"
+                        )
+                        continue
+                    else:
+                        break
+            break
+        else:
+            file_name = ""
+            print("\n*** File given does exist, try again ***\n")
+    if verbose:
+        print("\n" + file_name.split("/")[-1] + " opened")
+
+    return open(file_name, open_mode)
+
+
+def checkequal(iterator):
+    try:
+        iterator = iter(iterator)
+        first = next(iterator)
+        return all(first == rest for rest in iterator)
+    except StopIteration:
+        return True