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)
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)
# 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))
# 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))
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)