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Commit 5bba74303d5585b93b167010b5c83269d1cafa2c

Authored by Santiago Castro
1 parent 829e75d1
Exists in command-line

Add option to import every group of DICOM images

Showing 2 changed files with 57 additions and 12 deletions   Show diff stats
app.py
  Diff comments   View file @5bba743
... ... @@ -26,6 +26,8 @@ import sys
26 26 import shutil
27 27 import traceback
28 28  
  29 +import re
  30 +
29 31 if sys.platform == 'win32':
30 32 import _winreg
31 33 else:
... ... @@ -270,6 +272,9 @@ def parse_comand_line():
270 272 action="store",
271 273 dest="dicom_dir")
272 274  
  275 + parser.add_option("--import-all",
  276 + action="store")
  277 +
273 278 parser.add_option("-s", "--save",
274 279 help="Save the project after an import.")
275 280  
... ... @@ -296,7 +301,7 @@ def use_cmd_optargs(options, args):
296 301 # If import DICOM argument...
297 302 if options.dicom_dir:
298 303 import_dir = options.dicom_dir
299   - Publisher.sendMessage('Import directory', import_dir)
  304 + Publisher.sendMessage('Import directory', {'directory': import_dir, 'gui': not options.no_gui})
300 305  
301 306 if options.save:
302 307 Publisher.sendMessage('Save project', os.path.abspath(options.save))
... ... @@ -305,6 +310,14 @@ def use_cmd_optargs(options, args):
305 310 check_for_export(options)
306 311  
307 312 return True
  313 + elif options.import_all:
  314 + import invesalius.reader.dicom_reader as dcm
  315 + for patient in dcm.GetDicomGroups(options.import_all):
  316 + for group in patient.GetGroups():
  317 + Publisher.sendMessage('Import group', {'group': group, 'gui': not options.no_gui})
  318 + check_for_export(options, suffix=group.title, remove_surfaces=False)
  319 + Publisher.sendMessage('Remove masks', [0])
  320 + return True
308 321  
309 322 # Check if there is a file path somewhere in what the user wrote
310 323 # In case there is, try opening as it was a inv3
... ... @@ -320,13 +333,29 @@ def use_cmd_optargs(options, args):
320 333 return False
321 334  
322 335  
323   -def check_for_export(options):
  336 +def sanitize(text):
  337 + text = str(text).strip().replace(' ', '_')
  338 + return re.sub(r'(?u)[^-\w.]', '', text)
  339 +
  340 +
  341 +def check_for_export(options, suffix='', remove_surfaces=False):
  342 + suffix = sanitize(suffix)
  343 +
324 344 if options.export:
325 345 if not options.threshold:
326 346 print("Need option --threshold when using --export.")
327 347 exit(1)
328   - threshold_range = tuple([int(n) for n in options.threshold.split('-')])
329   - export(options.export, threshold_range)
  348 + threshold_range = tuple([int(n) for n in options.threshold.split(',')])
  349 +
  350 + if suffix:
  351 + if options.export.endswith('.stl'):
  352 + path_ = '{}-{}.stl'.format(options.export[:-4], suffix)
  353 + else:
  354 + path_ = '{}-{}.stl'.format(options.export, suffix)
  355 + else:
  356 + path_ = options.export
  357 +
  358 + export(path_, threshold_range, remove_surface=remove_surfaces)
330 359 elif options.export_to_all:
331 360 # noinspection PyBroadException
332 361 try:
... ... @@ -334,15 +363,15 @@ def check_for_export(options):
334 363  
335 364 for threshold_name, threshold_range in Project().presets.thresh_ct.iteritems():
336 365 if isinstance(threshold_range[0], int):
337   - path_ = u'{}-{}.stl'.format(options.export_to_all, threshold_name)
338   - export(path_, threshold_range)
  366 + path_ = u'{}-{}-{}.stl'.format(options.export_to_all, suffix, threshold_name)
  367 + export(path_, threshold_range, remove_surface=True)
339 368 except:
340 369 traceback.print_exc()
341 370 finally:
342 371 exit(0)
343 372  
344 373  
345   -def export(path_, threshold_range):
  374 +def export(path_, threshold_range, remove_surface=False):
346 375 import invesalius.constants as const
347 376  
348 377 Publisher.sendMessage('Set threshold values', threshold_range)
... ... @@ -362,6 +391,8 @@ def export(path_, threshold_range):
362 391 }
363 392 Publisher.sendMessage('Create surface from index', surface_options)
364 393 Publisher.sendMessage('Export surface to file', (path_, const.FILETYPE_STL))
  394 + if remove_surface:
  395 + Publisher.sendMessage('Remove surfaces', [0])
365 396  
366 397  
367 398 def print_events(data):
... ...
invesalius/control.py
  Diff comments   View file @5bba743
... ... @@ -61,6 +61,7 @@ class Controller():
61 61  
62 62 def __bind_events(self):
63 63 Publisher.subscribe(self.OnImportMedicalImages, 'Import directory')
  64 + Publisher.subscribe(self.OnImportGroup, 'Import group')
64 65 Publisher.subscribe(self.OnShowDialogImportDirectory,
65 66 'Show import directory dialog')
66 67 Publisher.subscribe(self.OnShowDialogImportOtherFiles,
... ... @@ -440,10 +441,11 @@ class Controller():
440 441 #----------- to import by command line ---------------------------------------------------
441 442  
442 443 def OnImportMedicalImages(self, pubsub_evt):
443   - directory = pubsub_evt.data
444   - self.ImportMedicalImages(directory)
  444 + directory = pubsub_evt.data['directory']
  445 + gui = pubsub_evt.data['gui']
  446 + self.ImportMedicalImages(directory, gui)
445 447  
446   - def ImportMedicalImages(self, directory):
  448 + def ImportMedicalImages(self, directory, gui=True):
447 449 patients_groups = dcm.GetDicomGroups(directory)
448 450 name = directory.rpartition('\\')[-1].split('.')
449 451 print "patients: ", patients_groups
... ... @@ -451,7 +453,7 @@ class Controller():
451 453 if len(patients_groups):
452 454 # OPTION 1: DICOM
453 455 group = dcm.SelectLargerDicomGroup(patients_groups)
454   - matrix, matrix_filename, dicom = self.OpenDicomGroup(group, 0, [0, 0], gui=True)
  456 + matrix, matrix_filename, dicom = self.OpenDicomGroup(group, 0, [0, 0], gui=gui)
455 457 self.CreateDicomProject(dicom, matrix, matrix_filename)
456 458 else:
457 459 # OPTION 2: NIfTI, Analyze or PAR/REC
... ... @@ -474,6 +476,18 @@ class Controller():
474 476 self.LoadProject()
475 477 Publisher.sendMessage("Enable state project", True)
476 478  
  479 + def OnImportGroup(self, pubsub_evt):
  480 + group = pubsub_evt.data['group']
  481 + gui = pubsub_evt.data['gui']
  482 + self.ImportGroup(group, gui)
  483 +
  484 + def ImportGroup(self, group, gui=True):
  485 + matrix, matrix_filename, dicom = self.OpenDicomGroup(group, 0, [0, 0], gui=gui)
  486 + self.CreateDicomProject(dicom, matrix, matrix_filename)
  487 +
  488 + self.LoadProject()
  489 + Publisher.sendMessage("Enable state project", True)
  490 +
477 491 #-------------------------------------------------------------------------------------
478 492  
479 493 def LoadProject(self):
... ... @@ -788,7 +802,7 @@ class Controller():
788 802 n_slices = len(filelist)
789 803 resolution_percentage = utils.calculate_resizing_tofitmemory(int(sx), int(sy), n_slices, bits/8)
790 804  
791   - if resolution_percentage < 1.0:
  805 + if resolution_percentage < 1.0 and gui:
792 806 re_dialog = dialog.ResizeImageDialog()
793 807 re_dialog.SetValue(int(resolution_percentage*100))
794 808 re_dialog_value = re_dialog.ShowModal()
... ...