PyMca5 5.9.6__tar.gz → 5.9.7rc2__tar.gz

{pymca5-5.9.6/src/PyMca5.egg-info → pymca5-5.9.7rc2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyMca5
-Version: 5.9.6
+Version: 5.9.7rc2
 Summary: Mapping and X-Ray Fluorescence Analysis
 Author: V. Armando Sole
 Author-email: sole@esrf.fr

{pymca5-5.9.6 → pymca5-5.9.7rc2}/src/PyMca5/PyMcaCore/LegacyStackROIBatch.py

@@ -33,11 +33,17 @@ __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
 __doc__ = """
 Module to calculate a set of ROIs on a stack of data.
 """
+
 import os
+import sys
+import logging
+
 import numpy
+
 from PyMca5.PyMcaIO import ConfigDict
-import time
-import logging
+from PyMca5.PyMca import EDFStack
+from PyMca5.PyMca import ArraySave
+from PyMca5.PyMcaMisc import CliUtils
 
 _logger = logging.getLogger(__name__)
 
@@ -274,113 +280,112 @@ def getFileListFromPattern(pattern, begin, end, increment=None):
         raise ValueError("Cannot handle more than three indices.")
     return fileList
 
-if __name__ == "__main__":
-    import glob
-    import sys
-    from PyMca5.PyMca import EDFStack
-    from PyMca5.PyMca import ArraySave
-    import getopt
-    _logger.setLevel(logging.DEBUG)
-    options     = ''
-    longoptions = ['cfg=', 'outdir=',
-                   'tif=', #'listfile=',
-                   'filepattern=', 'begin=', 'end=', 'increment=',
-                   "outfileroot="]
-    try:
-        opts, args = getopt.getopt(
-                     sys.argv[1:],
-                     options,
-                     longoptions)
-    except Exception:
-        _logger.error(sys.exc_info()[1])
-        sys.exit(1)
-    fileRoot = ""
-    outputDir = None
-    fileindex = 0
-    filepattern=None
-    begin = None
-    end = None
-    increment=None
-    tif=0
-    for opt, arg in opts:
-        if opt in ('--cfg'):
-            configurationFile = arg
-        elif opt in '--begin':
-            if "," in arg:
-                begin = [int(x) for x in arg.split(",")]
-            else:
-                begin = [int(arg)]
-        elif opt in '--end':
-            if "," in arg:
-                end = [int(x) for x in arg.split(",")]
-            else:
-                end = int(arg)
-        elif opt in '--increment':
-            if "," in arg:
-                increment = [int(x) for x in arg.split(",")]
-            else:
-                increment = int(arg)
-        elif opt in '--filepattern':
-            filepattern = arg.replace('"', '')
-            filepattern = filepattern.replace("'", "")
-        elif opt in '--outdir':
-            outputDir = arg
-        elif opt in '--outfileroot':
-            fileRoot = arg
-        elif opt in ['--tif', '--tiff']:
-            tif = int(arg)
-    if filepattern is not None:
-        if (begin is None) or (end is None):
-            raise ValueError(\
-                "A file pattern needs at least a set of begin and end indices")
-    if filepattern is not None:
-        fileList = getFileListFromPattern(filepattern, begin, end, increment=increment)
-    else:
-        fileList = args
-    if len(fileList):
-        dataStack = EDFStack.EDFStack(fileList, dtype=numpy.float32)
+
+def main(args):
+    if args.filepattern is not None:
+        if args.begin is None or args.end is None:
+            raise ValueError(
+                "A file pattern needs at least a set of begin and end indices"
+            )
+        fileList = getFileListFromPattern(
+            args.filepattern,
+            args.begin,
+            args.end,
+            increment=args.increment,
+        )
     else:
-        print("OPTIONS:", longoptions)
-        sys.exit(0)
-    if outputDir is None:
+        fileList = args.files
+
+    if not fileList:
+        print("No input files provided")
+        return 0
+
+    dataStack = EDFStack.EDFStack(fileList, dtype=numpy.float32)
+
+    if args.outdir is None:
         print("RESULTS WILL NOT BE SAVED: No output directory specified")
-    t0 = time.time()
+
     worker = StackROIBatch()
-    worker.setConfigurationFile(configurationFile)
+    worker.setConfigurationFile(args.configurationFile)
     result = worker.batchROIMultipleSpectra(y=dataStack)
-    if outputDir is not None:
-        imageNames = result['names']
-        images = result['images']
-        nImages = images.shape[0]
-
-        if fileRoot in [None, ""]:
-            fileRoot = "images"
-        if not os.path.exists(outputDir):
-            os.mkdir(outputDir)
-        imagesDir = os.path.join(outputDir, "IMAGES")
-        if not os.path.exists(imagesDir):
-            os.mkdir(imagesDir)
-        imageList = [None] * (nImages)
-        fileImageNames = [None] * (nImages)
-        j = 0
-        for i in range(nImages):
-            name = imageNames[i].replace(" ", "-")
-            fileImageNames[j] = name
-            imageList[j] = images[i]
-            j += 1
-        fileName = os.path.join(imagesDir, fileRoot+".edf")
-        ArraySave.save2DArrayListAsEDF(imageList, fileName,
-                                       labels=fileImageNames)
-        fileName = os.path.join(imagesDir, fileRoot+".csv")
-        ArraySave.save2DArrayListAsASCII(imageList, fileName, csv=True,
-                                         labels=fileImageNames)
-        if tif:
-            i = 0
-            for i in range(len(fileImageNames)):
-                label = fileImageNames[i]
-                fileName = os.path.join(imagesDir,
-                                        fileRoot + fileImageNames[i] + ".tif")
-                ArraySave.save2DArrayListAsMonochromaticTiff([imageList[i]],
-                                        fileName,
-                                        labels=[label],
-                                        dtype=numpy.float32)
+
+    if args.outdir is None:
+        print("No output directory provided")
+        return 0
+
+    imageNames = result["names"]
+    images = result["images"]
+    nImages = images.shape[0]
+
+    fileRoot = args.fileRoot
+    if not fileRoot:
+        fileRoot = "images"
+
+    os.makedirs(args.outdir, exist_ok=True)
+    imagesDir = os.path.join(args.outdir, "IMAGES")
+    os.makedirs(imagesDir, exist_ok=True)
+
+    imageList = []
+    fileImageNames = []
+
+    for i in range(nImages):
+        name = imageNames[i].replace(" ", "-")
+        fileImageNames.append(name)
+        imageList.append(images[i])
+
+    # Save EDF
+    fileName = os.path.join(imagesDir, fileRoot + ".edf")
+    ArraySave.save2DArrayListAsEDF(
+        imageList,
+        fileName,
+        labels=fileImageNames,
+    )
+
+    # Save CSV
+    fileName = os.path.join(imagesDir, fileRoot + ".csv")
+    ArraySave.save2DArrayListAsASCII(
+        imageList,
+        fileName,
+        csv=True,
+        labels=fileImageNames,
+    )
+
+    # Optional TIFF
+    if args.tif:
+        for i, label in enumerate(fileImageNames):
+            fileName = os.path.join(
+                imagesDir,
+                fileRoot + label + ".tif"
+            )
+            ArraySave.save2DArrayListAsMonochromaticTiff(
+                [imageList[i]],
+                fileName,
+                labels=[label],
+                dtype=numpy.float32,
+            )
+
+    return 0
+
+
+def build_parser():
+    parser = CliUtils.create_parser(description="Stack ROI Batch Processing")
+
+    parser.add_argument("--cfg", type=str, dest="configurationFile")
+    parser.add_argument("--outdir", type=str, default=None)
+    parser.add_argument("--outfileroot", type=str, dest="fileRoot", default=None)
+
+    parser.add_argument("--filepattern", type=str, default=None, help="File pattern")
+    parser.add_argument("--begin", type=CliUtils.int_or_list, default=None, help="Begin index/indices, comma-separated")
+    parser.add_argument("--end", type=CliUtils.int_or_list, default=None, help="End index/indices, comma-separated")
+    parser.add_argument("--increment", type=CliUtils.int_or_list, default=None, help="Increment(s), comma-separated")
+
+    parser.add_argument("--tif", type=int, default=0)
+
+    parser.add_argument("files", nargs="*")
+
+    return parser
+
+
+if __name__ == "__main__":
+    exit_code = CliUtils.cli_main(main, build_parser(), loggers=(_logger,))
+    sys.exit(exit_code)

{pymca5-5.9.6 → pymca5-5.9.7rc2}/src/PyMca5/PyMcaCore/McaStackExport.py

@@ -45,10 +45,7 @@ except Exception:
     HAS_NEXUS_UTILS = False
     _logger.info("PyMca5.PyMcaIO.NexusUtils could not be imported")
 
-if sys.version_info < (3,):
-    strdtype = h5py.special_dtype(vlen=unicode)
-else:
-    strdtype = h5py.special_dtype(vlen=str)
+strdtype = h5py.special_dtype(vlen=str)
 
 def exportStackList(stackList, filename, channels=None, calibration=None):
     if hasattr(stackList, "data") and hasattr(stackList, "info"):

{pymca5-5.9.6 → pymca5-5.9.7rc2}/src/PyMca5/PyMcaCore/McaStackView.py

@@ -27,7 +27,6 @@
 #
 #############################################################################*/
 __author__ = "Wout De Nolf"
-__contact__ = "wout.de_nolf@esrf.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
 

{pymca5-5.9.6 → pymca5-5.9.7rc2}/src/PyMca5/PyMcaCore/NexusDataSource.py

@@ -198,7 +198,7 @@ class NexusDataSource(object):
             try:
                 phynxInstance = h5open(name)
             except IOError:
-                if 'FAMILY DRIVER' in sys.exc_info()[1].args[0].upper():
+                if 'FAMILY DRIVER' in str(sys.exc_info()[1]).upper():
                     FAMILY = True
                 else:
                     raise
@@ -206,7 +206,7 @@ class NexusDataSource(object):
                 try:
                     phynxInstance = h5open(name)
                 except IOError:
-                    if 'FAMILY DRIVER' in sys.exc_info()[1].args[0].upper():
+                    if 'FAMILY DRIVER' in str(sys.exc_info()[1]).upper():
                         FAMILY = True
                     else:
                         raise
@@ -331,6 +331,9 @@ class NexusDataSource(object):
             _logger.warning(txt)
             output.info["title"] = ""
         output.info['selection'] = selection
+        # promote plot_yaxis from selection to top-level info so the right Y-axis could appear
+        if 'plot_yaxis' in selection:
+            output.info['plot_yaxis'] = selection['plot_yaxis']
         if entry != "/":
             try:
                 positioners = NexusTools.getPositionersGroup(phynxFile, entry)
@@ -604,8 +607,13 @@ class NexusDataSource(object):
                         data = phynxFile[path][()]
                         output.x.append(data)
             elif cnt == 'm':
-                #only one monitor
+                # support multiple monitors
                 output.m = [data]
+                if len(selection[cnt]) > 1:
+                    for midx in range(1, len(selection[cnt])):
+                        mpath = entry + selection['cntlist'][selection[cnt][midx]]
+                        mdata = phynxFile[mpath][()]
+                        output.m.append(mdata)
 
         # SCAN specific to handle asynchronous writing
         if output.info['selectiontype'] in ["1D"]:
@@ -617,9 +625,10 @@ class NexusDataSource(object):
                     delta = abs(ylength - xlength)
                     length = min(length, xlength)
                 if output.m:
-                    mlength = output.m[0].size
-                    delta = max(delta, ylength - mlength)
-                    length = min(length, mlength)
+                    for mi in range(len(output.m)):
+                        mlength = output.m[mi].size
+                        delta = max(delta, abs(ylength - mlength))
+                        length = min(length, mlength)
                 if delta > 1:
                     _logger.warning("Stripping last %d points" % delta)
                 elif delta == 1:

{pymca5-5.9.6 → pymca5-5.9.7rc2}/src/PyMca5/PyMcaCore/NexusTools.py

@@ -35,7 +35,7 @@ import os
 import posixpath
 try:
     # try to import hdf5plugin
-    if hdf5plugin not in sys.modules:
+    if "hdf5plugin" not in sys.modules:
         import hdf5plugin
 except Exception:
     # but do not crash just because of it

{pymca5-5.9.6 → pymca5-5.9.7rc2}/src/PyMca5/PyMcaCore/StackBase.py

@@ -41,6 +41,7 @@ import os
 import sys
 import glob
 import logging
+import copy
 
 logger = logging.getLogger(__name__)
 
@@ -167,11 +168,8 @@ class StackBase(object):
                         del self.pluginInstanceDict[plugin]
                     if plugin in sys.modules:
                         if hasattr(sys.modules[plugin], targetMethod):
-                            if sys.version < '3.0':
-                                reload(sys.modules[plugin])
-                            else:
-                                import imp
-                                imp.reload(sys.modules[plugin])
+                            import importlib
+                            importlib.reload(sys.modules[plugin])
                     else:
                         try:
                             __import__(plugin)

{pymca5-5.9.6 → pymca5-5.9.7rc2}/src/PyMca5/PyMcaCore/StackROIBatch.py

@@ -33,14 +33,18 @@ __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
 __doc__ = """
 Module to calculate a set of ROIs on a stack of data.
 """
+
 import os
-import numpy
+import sys
 import logging
 import copy
+
+import numpy
+
 from PyMca5.PyMcaIO import ConfigDict
 from PyMca5.PyMcaIO.OutputBuffer import OutputBuffer as OutputBufferBase
 from PyMca5.PyMcaCore import McaStackView
-
+from PyMca5.PyMcaMisc import CliUtils
 
 _logger = logging.getLogger(__name__)
 
@@ -347,113 +351,85 @@ def prepareDataStack(fileList):
     return dataStack
 
 
-def main():
-    import glob
-    import sys
-    import getopt
-    _logger.setLevel(logging.DEBUG)
-    options = ''
-    longoptions = ['cfg=', 'outdir=',
-                   'tif=', 'edf=', 'csv=', 'h5=', 'dat=',
-                   'filepattern=', 'begin=', 'end=', 'increment=',
-                   'outroot=', 'outentry=', 'outprocess=',
-                   'overwrite=', 'multipage=']
-    try:
-        opts, args = getopt.getopt(
-                     sys.argv[1:],
-                     options,
-                     longoptions)
-    except Exception:
-        _logger.error(sys.exc_info()[1])
-        sys.exit(1)
-    outputDir = None
-    outputRoot = ""
-    fileEntry = ""
-    fileProcess = ""
-    filepattern = None
-    begin = None
-    end = None
-    increment = None
-    tif = 0
-    edf = 0
-    csv = 0
-    h5 = 1
-    dat = 0
-    overwrite = 1
-    multipage = 0
-    for opt, arg in opts:
-        if opt in ('--cfg'):
-            configurationFile = arg
-        elif opt in '--begin':
-            if "," in arg:
-                begin = [int(x) for x in arg.split(",")]
-            else:
-                begin = [int(arg)]
-        elif opt in '--end':
-            if "," in arg:
-                end = [int(x) for x in arg.split(",")]
-            else:
-                end = int(arg)
-        elif opt in '--increment':
-            if "," in arg:
-                increment = [int(x) for x in arg.split(",")]
-            else:
-                increment = int(arg)
-        elif opt in '--filepattern':
-            filepattern = arg.replace('"', '')
-            filepattern = filepattern.replace("'", "")
-        elif opt in '--outdir':
-            outputDir = arg
-        elif opt == '--outroot':
-            outputRoot = arg
-        elif opt == '--outentry':
-            fileEntry = arg
-        elif opt == '--outprocess':
-            fileProcess = arg
-        elif opt in ('--tif', '--tiff'):
-            tif = int(arg)
-        elif opt == '--edf':
-            edf = int(arg)
-        elif opt == '--csv':
-            csv = int(arg)
-        elif opt == '--h5':
-            h5 = int(arg)
-        elif opt == '--dat':
-            dat = int(arg)
-        elif opt == '--overwrite':
-            overwrite = int(arg)
-        elif opt == '--multipage':
-            multipage = int(arg)
-    if filepattern is not None:
-        if (begin is None) or (end is None):
+def main(args):
+    if args.filepattern is not None:
+        if args.begin is None or args.end is None:
             raise ValueError(
-                "A file pattern needs at least a set of begin and end indices")
-    if filepattern is not None:
-        fileList = getFileListFromPattern(filepattern, begin, end,
-                                          increment=increment)
-    else:
-        fileList = args
-    if len(fileList):
-        dataStack = prepareDataStack(fileList)
+                "A file pattern needs at least a set of begin and end indices"
+            )
+        fileList = getFileListFromPattern(
+            args.filepattern,
+            args.begin,
+            args.end,
+            increment=args.increment
+        )
     else:
-        print("OPTIONS:", longoptions)
-        sys.exit(0)
-    if outputDir is None:
+        fileList = args.files
+
+    if not fileList:
+        print("No input files provided")
+        return 0
+
+    dataStack = prepareDataStack(fileList)
+
+    if args.outdir is None:
         print("RESULTS WILL NOT BE SAVED: No output directory specified")
+
     worker = StackROIBatch()
-    worker.setConfigurationFile(configurationFile)
-    outbuffer = OutputBuffer(outputDir=outputDir,
-                             outputRoot=outputRoot,
-                             fileEntry=fileEntry,
-                             fileProcess=fileProcess,
-                             tif=tif, edf=edf, csv=csv,
-                             h5=h5, dat=dat,
-                             multipage=multipage,
-                             overwrite=overwrite)
+    worker.setConfigurationFile(args.configurationFile)
+
+    outbuffer = OutputBuffer(
+        outputDir=args.outdir,
+        outputRoot=args.outroot,
+        fileEntry=args.outentry,
+        fileProcess=args.outprocess,
+        tif=args.tif,
+        edf=args.edf,
+        csv=args.csv,
+        h5=args.h5,
+        dat=args.dat,
+        multipage=args.multipage,
+        overwrite=args.overwrite,
+    )
+
     with outbuffer.saveContext():
-        worker.batchROIMultipleSpectra(y=dataStack,
-                                       outbuffer=outbuffer)
+        worker.batchROIMultipleSpectra(
+            y=dataStack,
+            outbuffer=outbuffer
+        )
+
+    return 0
+
+
+def build_parser():
+    parser = CliUtils.create_parser(description="Stack ROI Batch Processing")
+
+    parser.add_argument("--cfg", type=str, dest="configurationFile")
+
+    parser.add_argument("--outdir", type=str, default=None)
+    parser.add_argument("--outroot", type=str, default=None)
+    parser.add_argument("--outentry", type=str, default=None)
+    parser.add_argument("--outprocess", type=str, default=None)
+
+    parser.add_argument("--filepattern", type=str, default=None, help="File pattern")
+    parser.add_argument("--begin", type=CliUtils.int_or_list, default=None, help="Begin index/indices, comma-separated")
+    parser.add_argument("--end", type=CliUtils.int_or_list, help="End index/indices, comma-separated")
+    parser.add_argument("--increment", type=CliUtils.int_or_list, help="Increment(s), comma-separated")
+
+    parser.add_argument("--tif", type=int, default=0)
+    parser.add_argument("--edf", type=int, default=0)
+    parser.add_argument("--csv", type=int, default=0)
+    parser.add_argument("--h5", type=int, default=1)
+    parser.add_argument("--dat", type=int, default=0)
+
+    parser.add_argument("--overwrite", type=int, default=1)
+    parser.add_argument("--multipage", type=int, default=0)
+
+    parser.add_argument("files", nargs="*", help="Input files")
+
+    return parser
+
 
 if __name__ == "__main__":
-    logging.basicConfig(level=logging.INFO)
-    main()
+    exit_code = CliUtils.cli_main(main, build_parser(), loggers=(_logger,))
+    sys.exit(exit_code)