def sort_ipp(filenames):
"""STOP PRESS. This is currently incomplete. I'm waiting to see
what's going to happen with the IPPSorter in GDCM.
Given a list of filenames, make use of the gdcm scanner to sort
them all according to IPP.
@param filenames: list of full pathnames that you want to have
sorted.
@returns: tuple with (average z space,
"""
s = gdcm.Scanner()
# we need the IOP and the IPP tags
iop_tag = gdcm.Tag(0x0020, 0x0037)
s.AddTag(iop_tag)
ipp_tag = gdcm.Tag(0x0020, 0x0032)
s.AddTag(ipp_tag)
ret = s.Scan(filenames)
if not ret:
return (0, [])
for f in filenames:
mapping = s.GetMapping(f)
pttv = gdcm.PythonTagToValue(mapping)
pttv.Start()
while not pttv.IsAtEnd():
tag = pttv.GetCurrentTag()
val = pttv.GetCurrentValue()
def get_largest_subfnames(fnames):
fname_grps = []
s = gdcm.Scanner()
tag = gdcm.Tag(0x0020, 0x0037)
s.AddTag(tag)
s.Scan(fnames)
vals = s.GetValues()
for val in vals:
fname_grp = s.GetAllFilenamesFromTagToValue(tag, val)
fname_grps.append(fname_grp)
return max(fname_grps, key=lambda x: len(x))
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()
t1 = gdcm.Tag(0x8, 0x8)
t2 = gdcm.Tag(0x10, 0x10)
# Iterate over directory
d = gdcm.Directory()
nfiles = d.Load(directory)
if (nfiles == 0): sys.exit(1)
# System.Console.WriteLine( "Files:\n" + d.toString() );
filenames = d.GetFilenames()
# Get rid of any Warning while parsing the DICOM files
gdcm.Trace.WarningOff()
# instanciate Scanner:
s = gdcm.Scanner()
s.AddTag(t1)
s.AddTag(t2)
b = s.Scan(filenames)
if (not b): sys.exit(1)
print "success"
#print s
pttv = gdcm.PythonTagToValue(s.GetMapping(filenames[1]))
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
def _scan(self, paths):
"""Given a list combining filenames and directories, search
recursively to find all valid DICOM files. Build
dictionaries.
"""
# UIDs are unique for their domains. Patient ID for example
# is not unique.
# Instance UID (0008,0018)
# Patient ID (0010,0020)
# Study UID (0020,000D) - data with common procedural context
# Study description (0008,1030)
# Series UID (0020,000E)
# see http://public.kitware.com/pipermail/igstk-developers/
# 2006-March/000901.html for explanation w.r.t. number of
# frames; for now we are going to assume that this refers to
# the number of included slices (as is the case for the
# Toshiba 320 slice for example)
tag_to_symbol = {
(0x0008, 0x0018): 'instance_uid',
(0x0010, 0x0010): 'patient_name',
(0x0010, 0x0020): 'patient_id',
(0x0020, 0x000d): 'study_uid',
(0x0008, 0x1030): 'study_description',
(0x0008, 0x0020): 'study_date',
(0x0020, 0x000e): 'series_uid',
(0x0008, 0x103e): 'series_description',
(0x0008, 0x0060): 'modality', # fixed per series
(0x0028, 0x0008): 'number_of_frames',
(0x0028, 0x0010): 'rows',
(0x0028, 0x0011): 'columns'
}
# find list of unique and sorted filenames
filenames = self._helper_recursive_glob(paths)
s = gdcm.Scanner()
# add the tags we want to the scanner
for tag_tuple in tag_to_symbol:
tag = gdcm.Tag(*tag_tuple)
s.AddTag(tag)
# maps from study_uid to instance of Study
study_dict = {}
# we're going to break the filenames up into 10 blocks and
# scan each block separately in order to be able to give
# proper feedback to the user, and also to give the user the
# opportunity to interrupt the scan
num_files = len(filenames)
# no filenames, we return an empty dict.
if num_files == 0:
return study_dict
num_files_per_block = 100
num_blocks = num_files / num_files_per_block
if num_blocks == 0:
num_blocks = 1
blocklen = num_files / num_blocks
blockmod = num_files % num_blocks
block_lens = [blocklen] * num_blocks
if blockmod > 0:
block_lens += [blockmod]
file_idx = 0
progress = 0.0
# setup progress dialog
dlg = wx.ProgressDialog(
"DICOMBrowser",
"Scanning DICOM data",
maximum=100,
parent=self._view_frame,
style=wx.PD_CAN_ABORT
| wx.PD_APP_MODAL
| wx.PD_ELAPSED_TIME
| wx.PD_AUTO_HIDE
#| wx.PD_ESTIMATED_TIME
| wx.PD_REMAINING_TIME)
keep_going = True
error_occurred = False
# and now the processing loop can start
for block_len in block_lens:
# scan the current block of files
try:
self._helper_scan_block(
s, filenames[file_idx:file_idx + block_len], tag_to_symbol,
study_dict)
except Exception:
# error during scan, we have to kill the dialog and
# then re-raise the error
dlg.Destroy()
raise
# update file_idx for the next block
file_idx += block_len
# update progress counter
progress = int(100 * file_idx / float(num_files))
# and tell the progress dialog about our progress
# by definition, progress will be 100 at the end: if you
# add all blocklens together, you have to get 1
(keep_going, skip) = dlg.Update(progress)
if not keep_going:
# user has clicked cancel so we zero the dictionary
study_dict = {}
# and stop the for loop
break
# dialog needs to be taken care of
dlg.Destroy()
# return all the scanned data
return study_dict
