def _helper_recursive_glob(self, paths):
"""Given a combined list of files and directories, return a
combined list of sorted and unique fully-qualified filenames,
consisting of the supplied filenames and a recursive search
through all supplied directories.
"""
# we'll use this to keep all filenames unique
files_dict = {}
d = gdcm.Directory()
for path in paths:
if os.path.isdir(path):
# we have to cast path to str (it's usually unicode)
# else the gdcm wrappers error on "bad number of
# arguments to overloaded function"
d.Load(str(path), True)
# fromkeys creates a new dictionary with GetFilenames
# as keys; then update merges this dictionary with the
# existing files_dict
normed = [os.path.normpath(i) for i in d.GetFilenames()]
files_dict.update(dict.fromkeys(normed, 1))
elif os.path.isfile(path):
files_dict[os.path.normpath(path)] = 1
# now sort everything
filenames = files_dict.keys()
filenames.sort()
return filenames
def get_series_dict(dirpath):
directory = gdcm.Directory()
loaded = directory.Load(dirpath)
if not loaded: return {}
scanner = gdcm.Scanner()
seruid_tag = gdcm.Tag(0x0020, 0x000e)
scanner.AddTag(seruid_tag)
scanned = scanner.Scan(directory.GetFilenames())
if not scanned: return {}
uids = scanner.GetValues()
series_dict = {}
for uid in uids:
series_dict[uid] = scanner.GetAllFilenamesFromTagToValue(
seruid_tag, uid)
return series_dict
def TestScan(dirname, recursive=False):
# Check the dirname is indeed a directory
system = gdcm.System()
if not system.FileIsDirectory(dirname):
print "Need a directory"
sys.exit(1)
# Retrieve all the files within that dir (recursively?)
d = gdcm.Directory()
nfiles = d.Load(dirname, recursive)
print "done retrieving all the", nfiles, "files"
s = gdcm.Scanner()
t1 = gdcm.Tag(0x0020, 0x000d) # VR::UI
t2 = gdcm.Tag(0x0020, 0x000e) # VR::UI
t3 = gdcm.Tag(0x0028, 0x0011) # VR::US
# Some fun tags, with dual VR:
t4 = gdcm.Tag(0x0028, 0x0106) # VR::US_SS
t5 = gdcm.Tag(0x0028, 0x0107) # VR::US_SS
s.AddTag(t1)
s.AddTag(t2)
s.AddTag(t3)
s.AddTag(t4)
s.AddTag(t5)
b = s.Scan(d.GetFilenames())
if not b:
print "Scanner failed"
sys.exit(1)
# Raw Values found:
values = s.GetValues()
print "Values found for all tags are:"
print values
# get the main super-map :
mappings = s.GetMappings()
#file1 = d.GetFilenames()[0];
#print file1
#m1 = s.GetMapping( file1 )
#print m1
#print dir(m1)
#for k,v in m1.iteritems():
# print "item", k,v
# For each file get the value for tag t1:
for f in d.GetFilenames():
print "Working on:", f
mapping = s.GetMapping(f)
pttv = gdcm.PythonTagToValue(mapping)
# reset iterator to start position
pttv.Start()
# iterate until the end:
while (not pttv.IsAtEnd()):
# get current value for tag and associated value:
# if tag was not found, then it was simply not added to the internal std::map
# Warning value can be None
tag = pttv.GetCurrentTag()
value = pttv.GetCurrentValue()
print tag, "->", value
# increment iterator
pttv.Next()
reader.SetNumberOfScalarComponents(numberOfScalarComponents)
if __name__ == "__main__":
try:
filename = os.sys.argv[1]
except:
# failure
print "Need a filename"
sys.exit(1)
# setup reader
r = vtkgdcm.vtkGDCMThreadedImageReader()
r.FileLowerLeftOn()
#dir = vtkDirectory()
dir = gdcm.Directory()
# Did user pass in a directory:
system = gdcm.System()
if system.FileIsDirectory(filename):
nfiles = dir.Load(filename)
files = dir.GetFilenames()
# Need to construct full path out of the simple filename
fullpath = vtkStringArray()
for file in files:
fullpath.InsertNextValue(file)
r.SetFileNames(fullpath)
assert fullpath.GetNumberOfValues() # Need at least one file
ExecuteInformation(r, fullpath.GetValue(0),
fullpath.GetNumberOfValues())
r.AddObserver("ProgressEvent", PrintProgress)
def scanDir(self, strPath, s):
d = gdcm.Directory()
nfiles = d.Load(strPath)
if (nfiles == 0):
sys.exit(-1)
# No DICOM files in the directory
filenames = d.GetFilenames()
qDebug("The number of files to scan is " + str(len(filenames)))
# Define the set of tags we are interested in, may need more
t1 = gdcm.Tag(0x10, 0x20)
# Patient ID
t2 = gdcm.Tag(0x10, 0x10)
# Patient Name
t3 = gdcm.Tag(0x20, 0x10)
# Study ID
t4 = gdcm.Tag(0x20, 0x0d)
# Study Instance UID
t5 = gdcm.Tag(0x20, 0x0e)
# Series Instance UID
t6 = gdcm.Tag(0x20, 0x11)
# Series Number
t7 = gdcm.Tag(0x28, 0x08)
# Number of Frames
t8 = gdcm.Tag(0x20, 0x32)
# Image Position
t10 = gdcm.Tag(0x28, 0x30)
# Pixel Spacing
t11 = gdcm.Tag(0x20, 0x37)
# Image Orientation Patient
t12 = gdcm.Tag(0x28, 0x02)
# Samples per pixel
t13 = gdcm.Tag(0x28, 0x04)
# Photometric Interpretation
t14 = gdcm.Tag(0x28, 0x10)
# Rows
t15 = gdcm.Tag(0x28, 0x11)
# Column
t16 = gdcm.Tag(0x28, 0x101)
# BitStored
t17 = gdcm.Tag(0x02, 0x02)
# Media Storage SOP Class UID
t18 = gdcm.Tag(0x02, 0x03)
# Media Storage SOP Instance UID
t19 = gdcm.Tag(0x02, 0x10)
# Transfer Syntax
t20 = gdcm.Tag(0x08, 0x16)
# SOP Class UID
t21 = gdcm.Tag(0x08, 0x18)
# SOP Instance UID
t22 = gdcm.Tag(0x5200, 0x9229)
# Shared functional group
t23 = gdcm.Tag(0x5200, 0x9230)
# Per frame functional group
t24 = gdcm.Tag(0x0028, 0x1050)
# WindowCenter
t25 = gdcm.Tag(0x0028, 0x1051)
# WindowWidth
t26 = gdcm.Tag(0x0028, 0x1052)
# Rescale Intercept
t27 = gdcm.Tag(0x0028, 0x1053)
# Rescale Slope
t28 = gdcm.Tag(0x0028, 0x1054)
# Rescale Type
t29 = gdcm.Tag(0x0010, 0x0030)
# PatientBirthDate
t30 = gdcm.Tag(0x0010, 0x0040)
# PatientSex
t31 = gdcm.Tag(0x0008, 0x0020)
# Study Date
t32 = gdcm.Tag(0x0008, 0x1030)
# Study Description
s.AddTag(t1)
s.AddTag(t2)
s.AddTag(t3)
s.AddTag(t4)
s.AddTag(t5)
s.AddTag(t6)
s.AddTag(t7)
s.AddTag(t8)
s.AddTag(t10)
s.AddTag(t11)
s.AddTag(t12)
s.AddTag(t13)
s.AddTag(t14)
s.AddTag(t15)
s.AddTag(t16)
s.AddTag(t17)
s.AddTag(t18)
s.AddTag(t19)
s.AddTag(t20)
s.AddTag(t21)
s.AddTag(t22)
s.AddTag(t23)
s.AddTag(t29)
s.AddTag(t30)
s.AddTag(t31)
s.AddTag(t32)
b = s.Scan(filenames)
# if no files in this directory
dicomfiles = []
if (not b):
qDebug("Empty directory")
return dicomfiles
study_list = []
series_list = []
series_count = {}
image_count = {}
for aFile in filenames:
if (s.IsKey(aFile)): # existing DICOM file
# qDebug("Scan "+aFile)
is_multiframe = 0
pttv = gdcm.PythonTagToValue(s.GetMapping(aFile))
pttv.Start()
patient_DOB = ""
patient_sex = ""
study_description = ""
# iterate until the end:
while (not pttv.IsAtEnd()):
# get current value for tag and associated value:
# if tag was not found, then it was simply not added to the internal std::map
# Warning value can be None
tag = pttv.GetCurrentTag()
value = pttv.GetCurrentValue()
if (tag == t1):
#print ("PatientID->",value)
patient_id = value
elif (tag == t2):
#print ("PatientName->",value)
patient_name = value
elif (tag == t29):
# print ("PatientBirthDate->",value)
patient_DOB = value
elif (tag == t30):
patient_sex = value
elif (tag == t3):
# print ("StudyID->",value)
study_id = value
elif (tag == t4):
studyinstance_uid = value
elif (tag == t31):
# print ("StudyDate->",value)
study_date = value
elif (tag == t32):
study_description = value
elif (tag == t6):
series_num = value
# print ("SeriesNum->",value)
elif (tag == t5):
# print ("SeriesInstanceUID->",value)
seriesinstance_uid = value
elif (tag == t7):
# print ("NumberOfFrame->",value)
if (int(value) > 1):
is_multiframe = int(value)
else:
is_multiframe = 0
elif (tag == t19):
# print("Transfer Syntax->",value)
pass
elif (tag == t20):
# print("SOP Class UID->",value)
sopclass_uid = value
#sop_ClassName = sopclass_uid.GetName()
elif (tag == t21):
# print("SOP Instance UID->",value)
sopinstance_uid = value
# increment iterator
pttv.Next()
# new StudyInstanceUID
if (studyinstance_uid not in series_count.keys()):
# Add to the study_list
study_list.append([
patient_id, patient_name, patient_DOB, patient_sex,
study_id, studyinstance_uid, study_date,
study_description, 0
])
# Add count
series_count[studyinstance_uid] = 0
# new SeriesInstanceUID
if (seriesinstance_uid not in image_count.keys()):
# Add to the series_list
series_list.append([
study_id, studyinstance_uid, seriesinstance_uid,
series_num, sopclass_uid, sopinstance_uid, 0
])
# Add count
image_count[seriesinstance_uid] = 0
series_count[studyinstance_uid] += 1
if (is_multiframe == 0):
image_count[seriesinstance_uid] += 1
else:
image_count[seriesinstance_uid] += is_multiframe
# print(series_count)
# print(image_count)
# for each study_list items update series_count from series_count(studyinstance_uid)
for study in study_list:
study[8] = series_count[study[5]]
# for each series_list items update images_count from image_count(seriesinstance_uid)
for series in series_list:
series[6] = image_count[series[2]]
#print(study_list)
#print(series_list)
return study_list, series_list
import gdcm
import sys
def PrintProgress(object, event):
assert event == "ProgressEvent"
print "Progress:", object.GetProgress()
def MySort(ds1, ds2):
# compare ds1
return False
if __name__ == "__main__":
dirname = sys.argv[1]
d = gdcm.Directory()
d.Load(dirname)
print d
sorter = gdcm.Sorter()
sorter.SetSortFunction(MySort)
#sorter.AddObserver( "ProgressEvent", PrintProgress )
sorter.Sort(d.GetFilenames())
print "Sorter:"
print sorter
