tomwer 1.2.1__py3-none-any.whl → 1.3.12__py3-none-any.whl

tomwer/core/utils/spec.py

@@ -0,0 +1,263 @@
+import fileinput
+import logging
+import os
+
+import fabio.edfimage
+from lxml import etree
+from pyunitsystem import metricsystem
+
+
+_logger = logging.getLogger(__name__)
+
+
+def _getInformation(scan, refFile, information, _type, aliases=None):
+    """
+    Parse files contained in the given directory to get the requested
+    information
+
+    :param scan: directory containing the acquisition. Must be an absolute path
+    :param refFile: the refXXXX_YYYY which should contain information about the
+                    scan.
+    :return: the requested information or None if not found
+    """
+
+    def parseRefFile(filePath):
+        header = fabio.open(filePath).header
+        for k in aliases:
+            if k in header:
+                return _type(header[k])
+        return None
+
+    def parseXMLFile(filePath):
+        try:
+            for alias in info_aliases:
+                tree = etree.parse(filePath)
+                elmt = tree.find("acquisition/" + alias)
+                if elmt is None:
+                    continue
+                else:
+                    info = _type(elmt.text)
+                    if info == -1:
+                        return None
+                    else:
+                        return info
+        except etree.XMLSyntaxError as e:
+            _logger.warning(e)
+            return None
+
+    def parseInfoFile(filePath):
+        def extractInformation(text, alias):
+            text = text.replace(alias, "")
+            text = text.replace("\n", "")
+            text = text.replace(" ", "")
+            text = text.replace("=", "")
+            return _type(text)
+
+        info = None
+        f = open(filePath, "r")
+        line = f.readline()
+        while line:
+            for alias in info_aliases:
+                if alias in line:
+                    info = extractInformation(line, alias)
+                    break
+            line = f.readline()
+        f.close()
+        return info
+
+    info_aliases = [information]
+    if aliases is not None:
+        assert type(aliases) in (tuple, list)
+        [info_aliases.append(alias) for alias in aliases]
+
+    if not os.path.isdir(scan):
+        return None
+
+    if refFile is not None and os.path.isfile(refFile):
+        try:
+            info = parseRefFile(refFile)
+        except IOError as e:
+            _logger.warning(e)
+        else:
+            if info is not None:
+                return info
+
+    baseName = os.path.basename(scan)
+    infoFiles = [os.path.join(scan, baseName + ".info")]
+    infoOnDataVisitor = infoFiles[0].replace("lbsram", "", 1)
+    # hack to check in lbsram, would need to be removed to add some consistency
+    if os.path.isfile(infoOnDataVisitor):
+        infoFiles.append(infoOnDataVisitor)
+    for infoFile in infoFiles:
+        if os.path.isfile(infoFile) is True:
+            info = parseInfoFile(infoFile)
+            if info is not None:
+                return info
+
+    xmlFiles = [os.path.join(scan, baseName + ".xml")]
+    xmlOnDataVisitor = xmlFiles[0].replace("lbsram", "", 1)
+    # hack to check in lbsram, would need to be removed to add some consistency
+    if os.path.isfile(xmlOnDataVisitor):
+        xmlFiles.append(xmlOnDataVisitor)
+    for xmlFile in xmlFiles:
+        if os.path.isfile(xmlFile) is True:
+            info = parseXMLFile(xmlFile)
+            if info is not None:
+                return info
+
+    return None
+
+
+def getClosestEnergy(scan, refFile=None):
+    """
+    Parse files contained in the given directory to get information about the
+    incoming energy for the serie `iSerie`
+
+    :param scan: directory containing the acquisition
+    :param refFile: the refXXXX_YYYY which should contain information about the
+                    energy.
+    :return: the energy in keV or none if no energy found
+    """
+    return _getInformation(
+        os.path.abspath(scan),
+        refFile,
+        information="Energy",
+        aliases=["energy", "ENERGY"],
+        _type=float,
+    )
+
+
+def getTomo_N(scan):
+    """Return the number of radio taken"""
+    return _getInformation(
+        os.path.abspath(scan),
+        refFile=None,
+        information="TOMO_N",
+        _type=int,
+        aliases=["tomo_N", "Tomo_N"],
+    )
+
+
+def getDARK_N(scan):
+    return _getInformation(
+        os.path.abspath(scan),
+        refFile=None,
+        information="DARK_N",
+        _type=int,
+        aliases=["dark_N"],
+    )
+
+
+def rebaseParFile(_file, oldfolder, newfolder):
+    """Update the given .par file to replace oldfolder location by the newfolder.
+
+    .. warning:: make the replacement in place.
+
+    :param _file: par file to update
+    :param oldfolder: previous location of the .par file
+    :param newfolder: new location of the .par file
+    """
+    with fileinput.FileInput(_file, inplace=True, backup=".bak") as parfile:
+        for line in parfile:
+            line = line.rstrip().replace(oldfolder, newfolder, 1)
+            print(line)
+
+
+def getDim1Dim2(scan):
+    """
+
+    :param scan: path to the acquisition
+    :return: detector definition
+    :rtype: tuple of int
+    """
+    d1 = _getInformation(
+        scan=scan,
+        refFile=None,
+        information="Dim_1",
+        aliases=["projectionSize/DIM_1"],
+        _type=int,
+    )
+    d2 = _getInformation(
+        scan=scan,
+        refFile=None,
+        information="Dim_2",
+        aliases=["projectionSize/DIM_2"],
+        _type=int,
+    )
+    return d1, d2
+
+
+def getParametersFromParOrInfo(_file):
+    """
+    Create a dictionary from the file with the information name as keys and
+    their values as values
+    """
+    assert os.path.exists(_file) and os.path.isfile(_file)
+    ddict = {}
+    f = open(_file, "r")
+    lines = f.readlines()
+    for line in lines:
+        if "=" not in line:
+            continue
+        line_str = line.replace(" ", "")
+        line_str = line_str.rstrip("\n")
+        # remove on the line comments
+        if "#" in line_str:
+            line_str = line_str.split("#")[0]
+        if line_str == "":
+            continue
+        try:
+            key, value = line_str.split("=")
+        except ValueError:
+            _logger.error('fail to extract information from "%s"' % line_str)
+        else:
+            ddict[key.lower()] = value
+    return ddict
+
+
+def getFirstProjFile(scan):
+    """Return the first .edf containing a projection"""
+    if os.path.isdir(scan) is False:
+        return None
+    files = sorted(os.listdir(scan))
+
+    while (
+        len(files) > 0
+        and (files[0].startswith(os.path.basename(scan)) and files[0].endswith(".edf"))
+        is False
+    ):
+        files.remove(files[0])
+
+    if len(files) > 0:
+        return os.path.join(scan, files[0])
+    else:
+        return None
+
+
+def getPixelSize(scan):
+    """
+    Try to retrieve the pixel size from the set of files.
+
+    :return: the pixel size in meter or None
+    :rtype: None or float
+    """
+    if os.path.isdir(scan) is False:
+        return None
+    value = _getInformation(
+        scan=scan,
+        refFile=None,
+        information="PixelSize",
+        _type=float,
+        aliases=["pixelSize"],
+    )
+    if value is None:
+        parFile = os.path.join(scan, os.path.basename(scan) + ".par")
+        if os.path.exists(parFile):
+            ddict = getParametersFromParOrInfo(parFile)
+            if "IMAGE_PIXEL_SIZE_1".lower() in ddict:
+                value = float(ddict["IMAGE_PIXEL_SIZE_1".lower()])
+    # for now pixel size are stored in microns. We want to return them in meter
+    if value is not None:
+        return value * metricsystem.micrometer.value
+    else:
+        return None

tomwer/core/volume/edfvolume.py

@@ -86,11 +86,11 @@ class EDFVolume(_EDFVolume, TomwerVolumeBase, Dataset):
             file_prefix=self._volume_basename,
             metadata={
                 "name": self.url.file_path(),
-                "creation_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
-                "modification_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
+                "creation_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
+                "modification_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
             },
         )

tomwer/core/volume/hdf5volume.py

@@ -103,11 +103,11 @@ class HDF5Volume(_HDF5Volume, TomwerVolumeBase, Dataset):
             entry=self.url.data_path(),
             metadata={
                 "name": self.url.file_path(),
-                "creation_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
-                "modification_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
+                "creation_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
+                "modification_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
             },
         )

tomwer/core/volume/jp2kvolume.py

@@ -87,11 +87,11 @@ class JP2KVolume(_JP2KVolume, TomwerVolumeBase, Dataset):
             file_prefix=self._volume_basename,
             metadata={
                 "name": self.url.file_path(),
-                "creation_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
-                "modification_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
+                "creation_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
+                "modification_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
             },
         )

tomwer/core/volume/rawvolume.py

@@ -97,11 +97,11 @@ class RawVolume(_RawVolume, TomwerVolumeBase, Dataset):
             file_path=self.url.file_path(),
             metadata={
                 "name": self.url.file_path(),
-                "creation_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
-                "modification_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
+                "creation_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
+                "modification_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
             },
         )

tomwer/core/volume/tiffvolume.py

@@ -103,12 +103,12 @@ class TIFFVolume(_TIFFVolume, TomwerVolumeBase, Dataset):
             file_prefix=self._volume_basename,
             metadata={
                 "name": self.url.file_path(),
-                "creation_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
-                "modification_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
+                "creation_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
+                "modification_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
             },
         )
 
@@ -145,12 +145,12 @@ class MultiTIFFVolume(_MultiTIFFVolume, TomwerVolumeBase, Dataset):
             tiff_file=self.url.file_path(),
             metadata={
                 "name": self.url.file_path(),
-                "creation_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
-                "modification_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
+                "creation_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
+                "modification_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
             },
         )
 

tomwer/core/volume/volumefactory.py

@@ -38,7 +38,7 @@ from tomoscan.factory import Factory as _oVolumeFactory
 from tomoscan.identifier import BaseIdentifier, ScanIdentifier, VolumeIdentifier
 
 from tomwer.core.scan.edfscan import EDFTomoScan, EDFTomoScanIdentifier
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.volume import (
     EDFVolume,
     HDF5Volume,
@@ -156,7 +156,7 @@ class VolumeFactory(_oVolumeFactory):
             if tomo_type == VolumeIdentifier.TOMO_TYPE:
                 return HDF5Volume.from_identifier(identifier=identifier)
             elif tomo_type == ScanIdentifier.TOMO_TYPE:
-                return HDF5TomoScan.from_identifier(identifier=identifier)
+                return NXtomoScan.from_identifier(identifier=identifier)
             else:
                 raise NotImplementedError()
         elif scheme == "jp2k":