Beispiel #1
0
import os.path
from pprint import pprint
# dicom.debug()


if __name__ == "__main__":
    print("------------------------------------------------------------")
    print("Example program showing DICOMDIR contents, assuming standard")
    print("Patient -> Study -> Series -> Images hierarchy")
    print("------------------------------------------------------------")
    print()
    if len(sys.argv) > 1:
        filepath = sys.argv[1]
        if os.path.isdir(filepath):  # only gave directory, add standard name
            filepath = os.path.join(filepath, "DICOMDIR")
        dcmdir = dicom.read_dicomdir(filepath)
        base_dir = os.path.dirname(filepath)
    else:
        # Read standard "DICOMDIR" filename from current directory
        dcmdir = dicom.read_dicomdir()
        base_dir = "."

    for patrec in dcmdir.patient_records:
        print("Patient: {0.PatientID}: {0.PatientsName}".format(patrec))
        studies = patrec.children
        for study in studies:
            print(("    Study {0.StudyID}: {0.StudyDate}:"
                  " {0.StudyDescription}".format(study)))
            all_series = study.children
            for series in all_series:
                image_count = len(series.children)
Beispiel #2
0
    print "Patient -> Study -> Series -> Images hierarchy"

    print "------------------------------------------------------------"

    print

    if len(sys.argv) > 1:

        filepath = sys.argv[1]

        if os.path.isdir(filepath):  # only gave directory, add standard name

            filepath = os.path.join(filepath, "DICOMDIR")

        dcmdir = dicom.read_dicomdir(filepath)

        base_dir = os.path.dirname(filepath)

    else:

        # Read standard "DICOMDIR" filename from current directory

        dcmdir = dicom.read_dicomdir()

        base_dir = "."

    for patrec in dcmdir.patient_records:

        print "Patient: {0.PatientID}: {0.PatientsName}".format(patrec)
Beispiel #3
0
# test.py
"""Temporary test file for pydicom development; will change over revisions
as test various things
"""
# Copyright (c) 2013 Darcy Mason
# This file is part of pydicom, relased under an MIT-style license.
#    See the file license.txt included with this distribution, also
#    available at http://pydicom.googlecode.com
#

import dicom
# dicom.debug()

if __name__ == "__main__":
    dcmdir = dicom.read_dicomdir()
    for patrec in dcmdir.patient_records:
        print("Patient: {0.PatientID}: {0.PatientsName}".format(patrec))
        studies = patrec.children
        for study in studies:
            print("    Study {0.StudyID}: {0.StudyDate}:"
                  " {0.StudyDescription}".format(study))
            all_series = study.children
            for series in all_series:
                image_count = len(series.children)
                plural = ('', 's')[image_count > 1]
                print(" " * 8 +
                      "Series {0.SeriesNumber}: {0.SeriesDescription}"
                      " ({1} image{2})".format(series, image_count, plural))
Beispiel #4
0
# test.py
"""Temporary test file for pydicom development; will change over revisions
as test various things
"""
# Copyright (c) 2013 Darcy Mason
# This file is part of pydicom, relased under an MIT-style license.
#    See the file license.txt included with this distribution, also
#    available at http://pydicom.googlecode.com
#

import dicom
# dicom.debug()


if __name__ == "__main__":
    dcmdir = dicom.read_dicomdir()
    for patrec in dcmdir.patient_records:
        print "Patient: {0.PatientID}: {0.PatientsName}".format(patrec)
        studies = patrec.children
        for study in studies:
            print ("    Study {0.StudyID}: {0.StudyDate}:"
                   " {0.StudyDescription}".format(study))
            all_series = study.children
            for series in all_series:
                image_count = len(series.children)
                plural = ('', 's')[image_count > 1]
                print (" " * 8 + "Series {0.SeriesNumber}: {0.SeriesDescription}"
                       " ({1} image{2})".format(series, image_count, plural))
Beispiel #5
0
def main(argv=None):
    if argv is None:
        argv = sys.argv[1:]
    # parse input from command line
    args = create_parser().parse_args(argv)

    if os.path.isdir(args.filepath):  # only gave directory, add standard name
        filepath = os.path.join(args.filepath, "DICOMDIR")
    dcmdir = dicom.read_dicomdir(args.filepath)
    base_dir = os.path.dirname(args.filepath)

    for patrec in dcmdir.patient_records:
        print "Patient: {0.PatientID}: {0.PatientsName}".format(patrec)
        studies = patrec.children
        for study in studies:
            print(
                "  Study {0.StudyID}: {0.StudyDate}: "
                "{0.StudyDescription} ({0.StudyInstanceUID})".format(study))
            all_series = study.children
            for series in all_series:
                image_count = len(series.children)
                plural = ('', 's')[image_count > 1]

                # Write basic series info and image count

                # Put N/A in if no Series Description
                if 'SeriesDescription' not in series:
                    series.SeriesDescription = "N/A"
                print(
                    " " * 4 +
                    "Series {0.SeriesNumber}:  {0.Modality}: {0.SeriesDescription}"
                    " ({0.SeriesInstanceUID}, {1} image{2})".format(
                        series, image_count, plural))

                if args.verbosity > 0:
                    # Open and read something from each image, for demonstration purposes
                    # For simple quick overview of DICOMDIR, leave the following out
                    print " " * 8 + "Reading images..."
                    image_records = series.children
                    image_filenames = [
                        os.path.join(base_dir, *image_rec.ReferencedFileID)
                        for image_rec in image_records
                    ]

                    # slice_locations = [dicom.read_file(image_filename).SliceLocation
                    #                   for image_filename in image_filenames]

                    datasets = [
                        dicom.read_file(image_filename)
                        for image_filename in image_filenames
                    ]

                    patient_names = set(ds.PatientName for ds in datasets)
                    patient_IDs = set(ds.PatientID for ds in datasets)

                    # List the image filenames
                    print "\n" + " " * 8 + "Image filenames:"
                    print " " * 8,
                    pprint(image_filenames, indent=8)

                    # Expect all images to have same patient name, id
                    # Show the set of all names, IDs found (should each have one)
                    print(
                        " " * 8 + "Patient Names in images..: "
                        "{0:s}".format(patient_names))
                    print(
                        " " * 8 + "Patient IDs in images..:"
                        "{0:s}".format(patient_IDs))
    def __init__(self, parent, path=None, main=None):

        wx.Panel.__init__(self, parent, -1)
        self.main = main
        self._last_filename = None
        self._ds = None
        self._search_filter = None

        self.Bind(wx.EVT_SIZE, self.OnSize)

        self.tree = gizmos.TreeListCtrl(
            self,
            -1,
            style=wx.TR_DEFAULT_STYLE
            #| wx.TR_HAS_BUTTONS
            #| wx.TR_TWIST_BUTTONS
            #| wx.TR_ROW_LINES
            # | wx.TR_COLUMN_LINES
            #| wx.TR_NO_LINES
            | wx.TR_FULL_ROW_HIGHLIGHT)

        self._column_widths = [0, 0, 0, 0, 0]

        # list of files to load
        self.filenames = []
        # filename/title to give current selection
        self.filename = None
        self.canonical_series_name = 'DICOMDIR'

        isz = (16, 16)
        il = wx.ImageList(isz[0], isz[1])
        fldridx = il.Add(
            wx.ArtProvider_GetBitmap(wx.ART_FOLDER, wx.ART_OTHER, isz))
        fldropenidx = il.Add(
            wx.ArtProvider_GetBitmap(wx.ART_FILE_OPEN, wx.ART_OTHER, isz))
        fileidx = il.Add(
            wx.ArtProvider_GetBitmap(wx.ART_NORMAL_FILE, wx.ART_OTHER, isz))

        self.tree.SetImageList(il)
        self.il = il

        # create some columns
        self.tree.AddColumn("Series ID")
        self.tree.AddColumn("Modality")
        self.tree.AddColumn("Description")
        self.tree.AddColumn("Acquisition")
        self.tree.AddColumn("Image Count")
        self.tree.SetMainColumn(0)  # the one with the tree in it...

        self.tree.SetColumnWidth(1, wx.COL_WIDTH_AUTOSIZE)
        self.tree.SetColumnWidth(3, wx.COL_WIDTH_AUTOSIZE)
        self.tree.SetColumnWidth(4, wx.COL_WIDTH_AUTOSIZE)

        self.root = self.tree.AddRoot("Patient List")

        self.tree.SetItemImage(self.root,
                               fldridx,
                               which=wx.TreeItemIcon_Normal)
        self.tree.SetItemImage(self.root,
                               fldropenidx,
                               which=wx.TreeItemIcon_Expanded)

        if path is None:
            path = '/mnt/Users/jerem_000/Desktop/DICOM/DICOM/DICOMDIR'

        path = os.path.abspath(path)

        # Why is this path manipulation needed?
        if os.path.isdir(path):
            self.base_dir = os.path.abspath(os.path.join(path, '..'))
        else:
            self.base_dir = os.path.abspath(os.path.dirname(path))

        with wx.BusyCursor():

            try:
                self._full_ds = ds = dicom.read_dicomdir(path)
            except:
                logging.error("Unable to read '{}'".format(path))
                return

            self.filename = path

            # copied from ImageInfo.py ++
            encoding = ds.get('SpecificCharacterSet', 'utf-8')

            python_encoding = {
                '': 'iso8859',  # default character set for DICOM
                'ISO_IR 6': 'iso8859',  # alias for latin_1 too
                'ISO_IR 100': 'latin_1',
                'ISO 2022 IR 87': 'iso2022_jp',
                # XXX this mapping does not work on chrH32.dcm test files (but
                # no others do either)
                'ISO 2022 IR 13': 'iso2022_jp',
                # XXX chrI2.dcm -- does not quite work -- some chrs wrong. Need
                # iso_ir_149 python encoding
                'ISO 2022 IR 149': 'euc_kr',
                # from Chinese example, 2008 PS3.5 Annex J p1-4
                'ISO_IR 192': 'UTF8',
                'GB18030': 'GB18030',
                'ISO_IR 126': 'iso_ir_126',  # Greek
                'ISO_IR 127': 'iso_ir_127',  # Arab
                'ISO_IR 138': 'iso_ir_138',  # Hebrew
                'ISO_IR 144': 'iso_ir_144',  # Russian
            }
            # copied from ImageInfo.py --

            for patient in ds.patient_records:
                txt = patient.PatientName or '* No Patient Name *'
                self._column_widths[0] = max(self._column_widths[0],
                                             self.tree.GetTextExtent(txt)[0])
                data = wx.TreeItemData()
                data.SetData((patient, -1))
                child = self.tree.AppendItem(self.root, txt, data=data)
                self.tree.SetItemText(child, patient.PatientID, 1)

                studies = patient.children
                for study in studies:

                    encoding = study.get('SpecificCharacterSet', 'utf-8')
                    if encoding in python_encoding:
                        encoding = python_encoding[encoding]

                    txt = study.StudyID or '* No Study ID *'
                    self._column_widths[1] = max(
                        self._column_widths[1],
                        self.tree.GetTextExtent(txt)[0])
                    data = wx.TreeItemData()
                    data.SetData((study, -1))
                    child2 = self.tree.AppendItem(child, txt, data=data)
                    self.tree.SetItemText(child2, study.get('StudyDate', '--'),
                                          1)

                    try:
                        s = study.get('StudyDescription',
                                      '--').decode(encoding)
                    except:
                        s = '* Unprintable Study Description *'

                    self.tree.SetItemText(child2, s, 2)

                    all_series = study.children
                    for series in all_series:

                        image_records = series.children
                        acquisitions = {}

                        for rec in series.children:
                            if rec.DirectoryRecordType == 'IMAGE':
                                acq = rec.get('AcquisitionNumber', -1)
                                if acq not in acquisitions:
                                    acquisitions[acq] = 0
                                acquisitions[acq] += 1

                        txt = str(series.SeriesNumber)

                        series_desc = series.get('SeriesDescription',
                                                 '* No Series Description *')

                        # support multiple acquisitions
                        if len(acquisitions) == 1 and -1 in acquisitions:
                            data = wx.TreeItemData()
                            data.SetData((series, -1))
                            child3 = self.tree.AppendItem(
                                child2,
                                series_desc.decode(encoding),
                                data=data)
                            modality = series.get('Modality', '--')
                            self.tree.SetItemText(child3, modality, 1)
                            self.tree.SetItemText(child3,
                                                  series_desc.decode(encoding),
                                                  2)
                            self.tree.SetItemText(child3,
                                                  str(acquisitions[-1]), 4)
                        else:
                            for acq in acquisitions:
                                data = wx.TreeItemData()
                                data.SetData((series, acq))
                                child3 = self.tree.AppendItem(child2,
                                                              txt,
                                                              data=data)
                                modality = series.get('Modality', '--')
                                self.tree.SetItemText(child3, modality, 1)
                                self.tree.SetItemText(
                                    child3, series_desc.decode(encoding), 2)
                                self.tree.SetItemText(child3, str(acq), 3)
                                self.tree.SetItemText(child3,
                                                      str(acquisitions[acq]),
                                                      4)

            self.tree.Expand(self.root)

        self.tree.GetMainWindow().Bind(wx.EVT_RIGHT_UP, self.OnRightUp)
        self.tree.Bind(wx.EVT_TREE_ITEM_ACTIVATED, self.OnActivate)
        self.tree.Bind(wx.EVT_TREE_SEL_CHANGED, self.OnSelectionChanged)

        self.tree.Bind(wx.EVT_SIZE, self._onResize)
        self.tree.Bind(wx.EVT_LIST_COL_END_DRAG, self._onResize, self)
    def __init__(self, parent, path=None, main=None):

        wx.Panel.__init__(self, parent, -1)
        self.main = main
        self._last_filename = None
        self._ds = None
        self._search_filter = None

        self.Bind(wx.EVT_SIZE, self.OnSize)

        self.tree = gizmos.TreeListCtrl(self, -1, style=wx.TR_DEFAULT_STYLE
                                        #| wx.TR_HAS_BUTTONS
                                        #| wx.TR_TWIST_BUTTONS
                                        #| wx.TR_ROW_LINES
                                        # | wx.TR_COLUMN_LINES
                                        #| wx.TR_NO_LINES
                                        | wx.TR_FULL_ROW_HIGHLIGHT
                                        )

        self._column_widths = [0, 0, 0, 0, 0]

        # list of files to load
        self.filenames = []
        # filename/title to give current selection
        self.filename = None
        self.canonical_series_name = 'DICOMDIR'

        isz = (16, 16)
        il = wx.ImageList(isz[0], isz[1])
        fldridx = il.Add(
            wx.ArtProvider_GetBitmap(wx.ART_FOLDER, wx.ART_OTHER, isz))
        fldropenidx = il.Add(
            wx.ArtProvider_GetBitmap(wx.ART_FILE_OPEN, wx.ART_OTHER, isz))
        fileidx = il.Add(
            wx.ArtProvider_GetBitmap(wx.ART_NORMAL_FILE, wx.ART_OTHER, isz))

        self.tree.SetImageList(il)
        self.il = il

        # create some columns
        self.tree.AddColumn("Series ID")
        self.tree.AddColumn("Modality")
        self.tree.AddColumn("Description")
        self.tree.AddColumn("Acquisition")
        self.tree.AddColumn("Image Count")
        self.tree.SetMainColumn(0)  # the one with the tree in it...

        self.tree.SetColumnWidth(1, wx.COL_WIDTH_AUTOSIZE)
        self.tree.SetColumnWidth(3, wx.COL_WIDTH_AUTOSIZE)
        self.tree.SetColumnWidth(4, wx.COL_WIDTH_AUTOSIZE)

        self.root = self.tree.AddRoot("Patient List")

        self.tree.SetItemImage(
            self.root, fldridx, which=wx.TreeItemIcon_Normal)
        self.tree.SetItemImage(
            self.root, fldropenidx, which=wx.TreeItemIcon_Expanded)

        if path is None:
            path = '/mnt/Users/jerem_000/Desktop/DICOM/DICOM/DICOMDIR'

        path = os.path.abspath(path)

        # Why is this path manipulation needed?
        if os.path.isdir(path):
            self.base_dir = os.path.abspath(os.path.join(path, '..'))
        else:
            self.base_dir = os.path.abspath(os.path.dirname(path))

        with wx.BusyCursor():

            try:
                self._full_ds = ds = dicom.read_dicomdir(path)
            except:
                logging.error("Unable to read '{}'".format(path))
                return

            self.filename = path

            # copied from ImageInfo.py ++
            encoding = ds.get('SpecificCharacterSet', 'utf-8')

            python_encoding = {
                '': 'iso8859',           # default character set for DICOM
                'ISO_IR 6': 'iso8859',   # alias for latin_1 too
                'ISO_IR 100': 'latin_1',
                'ISO 2022 IR 87': 'iso2022_jp',
                # XXX this mapping does not work on chrH32.dcm test files (but
                # no others do either)
                'ISO 2022 IR 13': 'iso2022_jp',
                # XXX chrI2.dcm -- does not quite work -- some chrs wrong. Need
                # iso_ir_149 python encoding
                'ISO 2022 IR 149': 'euc_kr',
                # from Chinese example, 2008 PS3.5 Annex J p1-4
                'ISO_IR 192': 'UTF8',
                'GB18030': 'GB18030',
                'ISO_IR 126': 'iso_ir_126',  # Greek
                'ISO_IR 127': 'iso_ir_127',  # Arab
                'ISO_IR 138': 'iso_ir_138',  # Hebrew
                'ISO_IR 144': 'iso_ir_144',  # Russian
            }
            # copied from ImageInfo.py --

            for patient in ds.patient_records:
                txt = patient.PatientName or '* No Patient Name *'
                self._column_widths[0] = max(
                    self._column_widths[0], self.tree.GetTextExtent(txt)[0])
                data = wx.TreeItemData()
                data.SetData((patient, -1))
                child = self.tree.AppendItem(self.root, txt, data=data)
                self.tree.SetItemText(child, patient.PatientID, 1)

                studies = patient.children
                for study in studies:

                    encoding = study.get('SpecificCharacterSet', 'utf-8')
                    if encoding in python_encoding:
                        encoding = python_encoding[encoding]

                    txt = study.StudyID or '* No Study ID *'
                    self._column_widths[1] = max(
                        self._column_widths[1], self.tree.GetTextExtent(txt)[0])
                    data = wx.TreeItemData()
                    data.SetData((study, -1))
                    child2 = self.tree.AppendItem(child, txt, data=data)
                    self.tree.SetItemText(
                        child2, study.get('StudyDate', '--'), 1)

                    try:
                        s = study.get(
                            'StudyDescription', '--').decode(encoding)
                    except:
                        s = '* Unprintable Study Description *'

                    self.tree.SetItemText(child2, s, 2)

                    all_series = study.children
                    for series in all_series:

                        image_records = series.children
                        acquisitions = {}

                        for rec in series.children:
                            if rec.DirectoryRecordType == 'IMAGE':
                                acq = rec.get('AcquisitionNumber', -1)
                                if acq not in acquisitions:
                                    acquisitions[acq] = 0
                                acquisitions[acq] += 1

                        txt = str(series.SeriesNumber)

                        series_desc = series.get(
                            'SeriesDescription', '* No Series Description *')

                        # support multiple acquisitions
                        if len(acquisitions) == 1 and -1 in acquisitions:
                            data = wx.TreeItemData()
                            data.SetData((series, -1))
                            child3 = self.tree.AppendItem(
                                child2, series_desc.decode(encoding), data=data)
                            modality = series.get('Modality', '--')
                            self.tree.SetItemText(child3, modality, 1)
                            self.tree.SetItemText(
                                child3, series_desc.decode(encoding), 2)
                            self.tree.SetItemText(
                                child3, str(acquisitions[-1]), 4)
                        else:
                            for acq in acquisitions:
                                data = wx.TreeItemData()
                                data.SetData((series, acq))
                                child3 = self.tree.AppendItem(
                                    child2, txt, data=data)
                                modality = series.get('Modality', '--')
                                self.tree.SetItemText(child3, modality, 1)
                                self.tree.SetItemText(
                                    child3, series_desc.decode(encoding), 2)
                                self.tree.SetItemText(child3, str(acq), 3)
                                self.tree.SetItemText(
                                    child3, str(acquisitions[acq]), 4)

            self.tree.Expand(self.root)

        self.tree.GetMainWindow().Bind(wx.EVT_RIGHT_UP, self.OnRightUp)
        self.tree.Bind(wx.EVT_TREE_ITEM_ACTIVATED, self.OnActivate)
        self.tree.Bind(wx.EVT_TREE_SEL_CHANGED, self.OnSelectionChanged)

        self.tree.Bind(wx.EVT_SIZE, self._onResize)
        self.tree.Bind(wx.EVT_LIST_COL_END_DRAG, self._onResize, self)