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Commit 7f9956549b19837f11f10b899f07b8ae2bd9b6df

Authored by Thiago Franco de Moraes
1 parent 32eb467e
Exists in master

Using black and isort in some python files

Showing 3 changed files with 413 additions and 415 deletions   Show diff stats
invesalius/data/converters.py
  Diff comments   View file @7f99565
1   -#--------------------------------------------------------------------------
  1 +# --------------------------------------------------------------------------
2 2 # Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
3 3 # Copyright: (C) 2001 Centro de Pesquisas Renato Archer
4 4 # Homepage: http://www.softwarepublico.gov.br
5 5 # Contact: invesalius@cti.gov.br
6 6 # License: GNU - GPL 2 (LICENSE.txt/LICENCA.txt)
7   -#--------------------------------------------------------------------------
  7 +# --------------------------------------------------------------------------
8 8 # Este programa e software livre; voce pode redistribui-lo e/ou
9 9 # modifica-lo sob os termos da Licenca Publica Geral GNU, conforme
10 10 # publicada pela Free Software Foundation; de acordo com a versao 2
... ... @@ -15,16 +15,22 @@
15 15 # COMERCIALIZACAO ou de ADEQUACAO A QUALQUER PROPOSITO EM
16 16 # PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
17 17 # detalhes.
18   -#--------------------------------------------------------------------------
  18 +# --------------------------------------------------------------------------
19 19  
20 20 import gdcm
21 21 import numpy as np
22 22 import vtk
23   -
24 23 from vtk.util import numpy_support
25 24  
26 25  
27   -def to_vtk(n_array, spacing=(1.0, 1.0, 1.0), slice_number=0, orientation='AXIAL', origin=(0, 0, 0), padding=(0, 0, 0)):
  26 +def to_vtk(
  27 + n_array,
  28 + spacing=(1.0, 1.0, 1.0),
  29 + slice_number=0,
  30 + orientation="AXIAL",
  31 + origin=(0, 0, 0),
  32 + padding=(0, 0, 0),
  33 +):
28 34 if orientation == "SAGITTAL":
29 35 orientation = "SAGITAL"
30 36  
... ... @@ -38,14 +44,35 @@ def to_vtk(n_array, spacing=(1.0, 1.0, 1.0), slice_number=0, orientation='AXIAL'
38 44  
39 45 v_image = numpy_support.numpy_to_vtk(n_array.flat)
40 46  
41   - if orientation == 'AXIAL':
42   - extent = (0 - px , dx -1 - px, 0 - py, dy - 1 - py, slice_number - pz, slice_number + dz - 1 - pz)
43   - elif orientation == 'SAGITAL':
  47 + if orientation == "AXIAL":
  48 + extent = (
  49 + 0 - px,
  50 + dx - 1 - px,
  51 + 0 - py,
  52 + dy - 1 - py,
  53 + slice_number - pz,
  54 + slice_number + dz - 1 - pz,
  55 + )
  56 + elif orientation == "SAGITAL":
44 57 dx, dy, dz = dz, dx, dy
45   - extent = (slice_number - px, slice_number + dx - 1 - px, 0 - py, dy - 1 - py, 0 - pz, dz - 1 - pz)
46   - elif orientation == 'CORONAL':
  58 + extent = (
  59 + slice_number - px,
  60 + slice_number + dx - 1 - px,
  61 + 0 - py,
  62 + dy - 1 - py,
  63 + 0 - pz,
  64 + dz - 1 - pz,
  65 + )
  66 + elif orientation == "CORONAL":
47 67 dx, dy, dz = dx, dz, dy
48   - extent = (0 - px, dx - 1 - px, slice_number - py, slice_number + dy - 1 - py, 0 - pz, dz - 1 - pz)
  68 + extent = (
  69 + 0 - px,
  70 + dx - 1 - px,
  71 + slice_number - py,
  72 + slice_number + dy - 1 - py,
  73 + 0 - pz,
  74 + dz - 1 - pz,
  75 + )
49 76  
50 77 # Generating the vtkImageData
51 78 image = vtk.vtkImageData()
... ... @@ -76,7 +103,7 @@ def to_vtk_mask(n_array, spacing=(1.0, 1.0, 1.0), origin=(0.0, 0.0, 0.0)):
76 103 oz -= sz
77 104  
78 105 v_image = numpy_support.numpy_to_vtk(n_array.flat)
79   - extent = (0, dx - 1, 0, dy - 1, 0, dz - 1)
  106 + extent = (0, dx - 1, 0, dy - 1, 0, dz - 1)
80 107  
81 108 # Generating the vtkImageData
82 109 image = vtk.vtkImageData()
... ... @@ -99,9 +126,9 @@ def to_vtk_mask(n_array, spacing=(1.0, 1.0, 1.0), origin=(0.0, 0.0, 0.0)):
99 126  
100 127 def np_rgba_to_vtk(n_array, spacing=(1.0, 1.0, 1.0)):
101 128 dy, dx, dc = n_array.shape
102   - v_image = numpy_support.numpy_to_vtk(n_array.reshape(dy*dx, dc))
  129 + v_image = numpy_support.numpy_to_vtk(n_array.reshape(dy * dx, dc))
103 130  
104   - extent = (0, dx -1, 0, dy -1, 0, 0)
  131 + extent = (0, dx - 1, 0, dy - 1, 0, 0)
105 132  
106 133 # Generating the vtkImageData
107 134 image = vtk.vtkImageData()
... ... @@ -122,27 +149,34 @@ def np_rgba_to_vtk(n_array, spacing=(1.0, 1.0, 1.0)):
122 149 # Based on http://gdcm.sourceforge.net/html/ConvertNumpy_8py-example.html
123 150 def gdcm_to_numpy(image, apply_intercep_scale=True):
124 151 map_gdcm_np = {
125   - gdcm.PixelFormat.UINT8 :np.uint8,
126   - gdcm.PixelFormat.INT8 :np.int8,
127   - gdcm.PixelFormat.UINT12 :np.uint16,
128   - gdcm.PixelFormat.INT12 :np.int16,
129   - gdcm.PixelFormat.UINT16 :np.uint16,
130   - gdcm.PixelFormat.INT16 :np.int16,
131   - gdcm.PixelFormat.UINT32 :np.uint32,
132   - gdcm.PixelFormat.INT32 :np.int32,
133   - #gdcm.PixelFormat.FLOAT16:np.float16,
134   - gdcm.PixelFormat.FLOAT32:np.float32,
135   - gdcm.PixelFormat.FLOAT64:np.float64,
  152 + gdcm.PixelFormat.UINT8: np.uint8,
  153 + gdcm.PixelFormat.INT8: np.int8,
  154 + gdcm.PixelFormat.UINT12: np.uint16,
  155 + gdcm.PixelFormat.INT12: np.int16,
  156 + gdcm.PixelFormat.UINT16: np.uint16,
  157 + gdcm.PixelFormat.INT16: np.int16,
  158 + gdcm.PixelFormat.UINT32: np.uint32,
  159 + gdcm.PixelFormat.INT32: np.int32,
  160 + # gdcm.PixelFormat.FLOAT16:np.float16,
  161 + gdcm.PixelFormat.FLOAT32: np.float32,
  162 + gdcm.PixelFormat.FLOAT64: np.float64,
136 163 }
137 164  
138 165 pf = image.GetPixelFormat()
139 166 if image.GetNumberOfDimensions() == 3:
140   - shape = image.GetDimension(2), image.GetDimension(1), image.GetDimension(0), pf.GetSamplesPerPixel()
  167 + shape = (
  168 + image.GetDimension(2),
  169 + image.GetDimension(1),
  170 + image.GetDimension(0),
  171 + pf.GetSamplesPerPixel(),
  172 + )
141 173 else:
142 174 shape = image.GetDimension(1), image.GetDimension(0), pf.GetSamplesPerPixel()
143 175 dtype = map_gdcm_np[pf.GetScalarType()]
144 176 gdcm_array = image.GetBuffer()
145   - np_array = np.frombuffer(gdcm_array.encode('utf-8', errors="surrogateescape"), dtype=dtype)
  177 + np_array = np.frombuffer(
  178 + gdcm_array.encode("utf-8", errors="surrogateescape"), dtype=dtype
  179 + )
146 180 np_array.shape = shape
147 181 np_array = np_array.squeeze()
148 182  
... ...
invesalius/reader/dicom.py
  Diff comments   View file @7f99565
1   -#---------------------------------------------------------------------
  1 +# ---------------------------------------------------------------------
2 2 # Software: InVesalius Software de Reconstrucao 3D de Imagens Medicas
3 3 # Copyright: (c) 2001 Centro de Pesquisas Renato Archer
4 4 # Homepage: http://www.softwarepublico.gov.br
... ... @@ -16,12 +16,14 @@
16 16 # COMERCIALIZACAO ou de ADEQUACAO A QUALQUER PROPOSITO EM
17 17 # PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
18 18 # detalhes.
19   -#---------------------------------------------------------------------
20   -import time
21   -#import gdcm
  19 +# ---------------------------------------------------------------------
  20 +# import gdcm
22 21 import sys
23   -import invesalius.utils as utils
  22 +import time
  23 +
24 24 import invesalius.constants as const
  25 +import invesalius.utils as utils
  26 +
25 27 # In DICOM file format, if multiple values are present for the
26 28 # "Window Center" (Level) and "Window Width", both attributes
27 29 # shall have the same number of values and shall be considered as
... ... @@ -30,48 +32,49 @@ import invesalius.constants as const
30 32 # one pair per time. This pair is determined by WL_PRESET
31 33 # constant or might be set by the user when calling GetWindowWidth
32 34 # and GetWindowLevel.
33   -WL_PRESET = 0 # index of selected window and level tuple (if multiple)
34   -WL_MULT = 0 # allow selection of multiple window and level tuples if 1
  35 +WL_PRESET = 0 # index of selected window and level tuple (if multiple)
  36 +WL_MULT = 0 # allow selection of multiple window and level tuples if 1
35 37  
36 38 # dictionary to be used by module functions
37 39 info = {}
38 40 # keys to be used to generate dictionary info
39   -INFO_KEYS = \
40   -['AcquisitionDate',
41   - 'AcquisitionGantryTilt',
42   - 'AcquisitionModality',
43   - 'AcquisitionNumber',
44   - 'AcquisionSequence',
45   - 'AcquisitionTime',
46   - 'EquipmentKVP',
47   - 'EquipmentInstitutionName',
48   - 'EquipmentManufacturer',
49   - 'EquipmentXRayTubeCurrent',
50   - 'ImageColumnOrientation',
51   - 'ImageConvolutionKernel',
52   - 'ImageDataType',
53   - 'ImageLocation',
54   - 'ImageNumber',
55   - 'ImagePixelSpacingX',
56   - 'ImagePixelSpacingY',
57   - 'ImagePosition',
58   - 'ImageRowOrientation',
59   - 'ImageSamplesPerPixel',
60   - 'ImageSeriesNumber',
61   - 'ImageThickness',
62   - 'ImageWindowLevel',
63   - 'ImageWindowWidth',
64   - 'PatientAge',
65   - 'PatientBirthDate',
66   - 'PatientGender',
67   - 'PatientName',
68   - 'PhysicianName',
69   - 'StudyID',
70   - 'StudyInstanceUID',
71   - 'StudyAdmittingDiagnosis',
72   - ]
73   -
74   -class Parser():
  41 +INFO_KEYS = [
  42 + "AcquisitionDate",
  43 + "AcquisitionGantryTilt",
  44 + "AcquisitionModality",
  45 + "AcquisitionNumber",
  46 + "AcquisionSequence",
  47 + "AcquisitionTime",
  48 + "EquipmentKVP",
  49 + "EquipmentInstitutionName",
  50 + "EquipmentManufacturer",
  51 + "EquipmentXRayTubeCurrent",
  52 + "ImageColumnOrientation",
  53 + "ImageConvolutionKernel",
  54 + "ImageDataType",
  55 + "ImageLocation",
  56 + "ImageNumber",
  57 + "ImagePixelSpacingX",
  58 + "ImagePixelSpacingY",
  59 + "ImagePosition",
  60 + "ImageRowOrientation",
  61 + "ImageSamplesPerPixel",
  62 + "ImageSeriesNumber",
  63 + "ImageThickness",
  64 + "ImageWindowLevel",
  65 + "ImageWindowWidth",
  66 + "PatientAge",
  67 + "PatientBirthDate",
  68 + "PatientGender",
  69 + "PatientName",
  70 + "PhysicianName",
  71 + "StudyID",
  72 + "StudyInstanceUID",
  73 + "StudyAdmittingDiagnosis",
  74 +]
  75 +
  76 +
  77 +class Parser:
75 78 """
76 79 Medical image parser. Used to parse medical image tags.
77 80 It supports:
... ... @@ -92,13 +95,13 @@ class Parser():
92 95 self.encoding = ""
93 96 self.filepath = ""
94 97  
95   - #def SetFileName(self, filename):
  98 + # def SetFileName(self, filename):
96 99 """
97 100 Set file name to be parsed given its filename (this should
98 101 include the full path of the file of interest).
99 102  
100 103 Return True/False if file could be read.
101   -
  104 +
102 105 import os.path as path
103 106  
104 107  
... ... @@ -134,28 +137,26 @@ class Parser():
134 137  
135 138 return False"""
136 139  
137   - #def GetImageData(self):
  140 + # def GetImageData(self):
138 141 # return None#self.vtkgdcm_reader.GetOutput()
139 142  
140   -
141 143 def SetDataImage(self, data_image, filename, thumbnail_path):
142 144 self.data_image = data_image
143 145 self.filename = self.filepath = filename
144 146 self.thumbnail_path = thumbnail_path
145 147  
146   - def __format_time(self,value):
  148 + def __format_time(self, value):
147 149 sp1 = value.split(".")
148 150 sp2 = value.split(":")
149 151  
150   - if (len(sp1) == 2) and (len(sp2) == 3):
151   - new_value = str(sp2[0]+sp2[1]+
152   - str(int(float(sp2[2]))))
  152 + if (len(sp1) == 2) and (len(sp2) == 3):
  153 + new_value = str(sp2[0] + sp2[1] + str(int(float(sp2[2]))))
153 154 data = time.strptime(new_value, "%H%M%S")
154   - elif (len(sp1) == 2):
  155 + elif len(sp1) == 2:
155 156 data = time.gmtime(float(value))
156   - elif (len(sp1) > 2):
  157 + elif len(sp1) > 2:
157 158 data = time.strptime(value, "%H.%M.%S")
158   - elif(len(sp2) > 1):
  159 + elif len(sp2) > 1:
159 160 data = time.strptime(value, "%H:%M:%S")
160 161 else:
161 162 try:
... ... @@ -163,26 +164,26 @@ class Parser():
163 164 # If the time is not in a bad format only return it.
164 165 except ValueError:
165 166 return value
166   - return time.strftime("%H:%M:%S",data)
  167 + return time.strftime("%H:%M:%S", data)
167 168  
168 169 def __format_date(self, value):
169 170  
170 171 sp1 = value.split(".")
171 172 try:
172 173  
173   - if (len(sp1) > 1):
174   - if (len(sp1[0]) <= 2):
  174 + if len(sp1) > 1:
  175 + if len(sp1[0]) <= 2:
175 176 data = time.strptime(value, "%D.%M.%Y")
176 177 else:
177 178 data = time.strptime(value, "%Y.%M.%d")
178   - elif(len(value.split("//")) > 1):
  179 + elif len(value.split("//")) > 1:
179 180 data = time.strptime(value, "%D/%M/%Y")
180 181 else:
181 182 data = time.strptime(value, "%Y%M%d")
182   - return time.strftime("%d/%M/%Y",data)
  183 + return time.strftime("%d/%M/%Y", data)
183 184  
184   - except(ValueError):
185   - return ""
  185 + except (ValueError):
  186 + return ""
186 187  
187 188 def GetImageOrientationLabel(self):
188 189 """
... ... @@ -190,9 +191,9 @@ class Parser():
190 191 an image. (AXIAL, SAGITTAL, CORONAL,
191 192 OBLIQUE or UNKNOWN)
192 193 """
193   - label = self.data_image['invesalius']['orientation_label']
  194 + label = self.data_image["invesalius"]["orientation_label"]
194 195  
195   - if (label):
  196 + if label:
196 197 return label
197 198 else:
198 199 return ""
... ... @@ -204,11 +205,10 @@ class Parser():
204 205 Return "" if not defined.
205 206 """
206 207 data = self.data_image[str(0x028)][str(0x011)]
207   - if (data):
  208 + if data:
208 209 return int(str(data))
209 210 return ""
210 211  
211   -
212 212 def GetDimensionY(self):
213 213 """
214 214 Return integer associated to Y dimension. This is related
... ... @@ -216,12 +216,11 @@ class Parser():
216 216 Return "" if not defined.
217 217 """
218 218 data = self.data_image[str(0x028)][str(0x010)]
219   - if (data):
  219 + if data:
220 220 return int(str(data))
221 221 return ""
222 222  
223   -
224   - #def GetDimensionZ(self):
  223 + # def GetDimensionZ(self):
225 224 # """
226 225 # Return float value associated to Z dimension.
227 226 # Return "" if not defined.
... ... @@ -291,7 +290,6 @@ class Parser():
291 290 return spacing[0]
292 291 return ""
293 292  
294   -
295 293 def GetAcquisitionDate(self):
296 294 """
297 295 Return string containing the acquisition date using the
... ... @@ -302,11 +300,11 @@ class Parser():
302 300 """
303 301 # TODO: internationalize data
304 302 try:
305   - date = self.data_image[str(0x0008)][str(0x0022)]
306   - except(KeyError):
  303 + date = self.data_image[str(0x0008)][str(0x0022)]
  304 + except (KeyError):
307 305 return ""
308 306  
309   - if (date) and (date != ''):
  307 + if (date) and (date != ""):
310 308 return self.__format_date(str(date))
311 309 return ""
312 310  
... ... @@ -317,8 +315,8 @@ class Parser():
317 315  
318 316 DICOM standard tag (0x0020, 0x0012) was used.
319 317 """
320   - data = self.data_image[str(0x0020)][str(0x0012)]
321   - if (data):
  318 + data = self.data_image[str(0x0020)][str(0x0012)]
  319 + if data:
322 320 return int(str(data))
323 321 return ""
324 322  
... ... @@ -328,12 +326,12 @@ class Parser():
328 326  
329 327 DICOM standard tag (0x0008, 0x0050) was used.
330 328 """
331   - #data = self.data_image[0x008][0x050]
  329 + # data = self.data_image[0x008][0x050]
332 330 return ""
333   - if (data):
  331 + if data:
334 332 try:
335 333 value = int(str(data))
336   - except(ValueError): #Problem in the other\iCatDanielaProjeto
  334 + except (ValueError): # Problem in the other\iCatDanielaProjeto
337 335 value = 0
338 336 return value
339 337 return ""
... ... @@ -347,7 +345,7 @@ class Parser():
347 345 DICOM standard tag (0x0008,0x0032) was used.
348 346 """
349 347 data = self.data_image[str(0x008)][str(0x032)]
350   - if (data) and (data != ''):
  348 + if (data) and (data != ""):
351 349 return self.__format_time(str(data))
352 350 return ""
353 351  
... ... @@ -363,11 +361,10 @@ class Parser():
363 361 sf.SetFile(self.gdcm_reader.GetFile())
364 362 res = sf.ToStringPair(tag)
365 363  
366   - if (res[1]):
  364 + if res[1]:
367 365 return int(res[1])
368 366 return ""
369 367  
370   -
371 368 def GetImageWindowLevel(self, preset=WL_PRESET, multiple=WL_MULT):
372 369 """
373 370 Return image window center / level (related to brightness).
... ... @@ -382,15 +379,15 @@ class Parser():
382 379 """
383 380 try:
384 381 data = self.data_image[str(0x028)][str(0x1050)]
385   - except(KeyError):
  382 + except (KeyError):
386 383 return "300"
387   - if (data):
  384 + if data:
388 385 # Usually 'data' is a number. However, in some DICOM
389 386 # files, there are several values separated by '\'.
390 387 # If multiple values are present for the "Window Center"
391 388 # we choose only one. As this should be paired to "Window
392 389 # Width", it is set based on WL_PRESET
393   - value_list = [float(value) for value in data.split('\\')]
  390 + value_list = [float(value) for value in data.split("\\")]
394 391 if multiple:
395 392 return value_list
396 393 else:
... ... @@ -414,16 +411,16 @@ class Parser():
414 411 """
415 412 try:
416 413 data = self.data_image[str(0x028)][str(0x1051)]
417   - except(KeyError):
  414 + except (KeyError):
418 415 return "2000"
419 416  
420   - if (data):
  417 + if data:
421 418 # Usually 'data' is a number. However, in some DICOM
422 419 # files, there are several values separated by '\'.
423 420 # If multiple values are present for the "Window Center"
424 421 # we choose only one. As this should be paired to "Window
425 422 # Width", it is set based on WL_PRESET
426   - value_list = [float(value) for value in data.split('\\')]
  423 + value_list = [float(value) for value in data.split("\\")]
427 424  
428 425 if multiple:
429 426 return str(value_list)
... ... @@ -443,10 +440,10 @@ class Parser():
443 440 """
444 441 try:
445 442 data = self.data_image[str(0x020)][str(0x032)].replace(",", ".")
446   - except(KeyError):
  443 + except (KeyError):
447 444 return ""
448   - if (data):
449   - return [eval(value) for value in data.split('\\')]
  445 + if data:
  446 + return [eval(value) for value in data.split("\\")]
450 447 return ""
451 448  
452 449 def GetImageLocation(self):
... ... @@ -458,7 +455,7 @@ class Parser():
458 455 DICOM standard tag (0x0020, 0x0032) was used.
459 456 """
460 457 data = self.data_image[str(0x020)][str(0x1041)]
461   - if (data):
  458 + if data:
462 459 return eval(data)
463 460 return ""
464 461  
... ... @@ -470,15 +467,14 @@ class Parser():
470 467 DICOM standard tag (0x7fe0, 0x0010) was used.
471 468 """
472 469 try:
473   - data = self.data_image[str(0x7fe0)][str(0x0010)]
474   - except(KeyError):
  470 + data = self.data_image[str(0x7FE0)][str(0x0010)]
  471 + except (KeyError):
475 472 return ""
476 473  
477   - if (data):
478   - return int(data.split(':')[1])
  474 + if data:
  475 + return int(data.split(":")[1])
479 476 return ""
480 477  
481   -
482 478 def GetImageSeriesNumber(self):
483 479 """
484 480 Return integer related to acquisition series where this
... ... @@ -489,14 +485,13 @@ class Parser():
489 485 """
490 486 try:
491 487 data = self.data_image[str(0x020)][str(0x011)]
492   - except(KeyError):
  488 + except (KeyError):
493 489 return ""
494 490  
495 491 if (data) and (data != '""') and (data != "None"):
496 492 return int(data)
497 493 return ""
498 494  
499   -
500 495 def GetPixelSpacing(self):
501 496 """
502 497 Return [x, y] (number list) related to the distance between
... ... @@ -508,7 +503,7 @@ class Parser():
508 503 DICOM standard tag (0x0028, 0x0030) was used.
509 504 """
510 505 try:
511   - image_helper_spacing = self.data_image["spacing"]
  506 + image_helper_spacing = self.data_image["spacing"]
512 507 except KeyError:
513 508 image_helper_spacing = None
514 509 try:
... ... @@ -516,7 +511,9 @@ class Parser():
516 511 except KeyError:
517 512 tag_spacing = ""
518 513  
519   - # Some dicom images have comma (,) as decimal separation. In this case InVesalius is not using the spacing given by gdcm.ImageHelper but using direct from the tag and replacing the comma with dot.
  514 + # Some dicom images have comma (,) as decimal separation. In this case
  515 + # InVesalius is not using the spacing given by gdcm.ImageHelper but
  516 + # using direct from the tag and replacing the comma with dot.
520 517 if image_helper_spacing is not None and "," not in tag_spacing:
521 518 return image_helper_spacing[:2]
522 519 else:
... ... @@ -531,10 +528,10 @@ class Parser():
531 528 """
532 529 try:
533 530 data = self.data_image[str(0x0010)][str(0x1030)]
534   - except(KeyError):
  531 + except (KeyError):
535 532 return ""
536 533  
537   - if (data):
  534 + if data:
538 535 return float(data)
539 536 return ""
540 537  
... ... @@ -547,10 +544,10 @@ class Parser():
547 544 """
548 545 try:
549 546 data = self.data_image[str(0x010)][str(0x1020)]
550   - except(KeyError):
  547 + except (KeyError):
551 548 return ""
552 549  
553   - if (data):
  550 + if data:
554 551 return float(data)
555 552 return ""
556 553  
... ... @@ -562,9 +559,9 @@ class Parser():
562 559 """
563 560 try:
564 561 data = self.data_image[str(0x010)][str(0x1040)]
565   - except(KeyError):
  562 + except (KeyError):
566 563 return ""
567   - if (data):
  564 + if data:
568 565 return data
569 566 return ""
570 567  
... ... @@ -577,9 +574,9 @@ class Parser():
577 574 """
578 575 try:
579 576 data = self.data_image[str(0x010)][str(0x1080)]
580   - except(KeyError):
  577 + except (KeyError):
581 578 return ""
582   - if (data):
  579 + if data:
583 580 return data
584 581 return ""
585 582  
... ... @@ -594,9 +591,9 @@ class Parser():
594 591 """
595 592 try:
596 593 data = self.data_image[str(0x010)][str(0x1081)]
597   - except(KeyError):
  594 + except (KeyError):
598 595 return ""
599   - if (data):
  596 + if data:
600 597 return data
601 598 return ""
602 599  
... ... @@ -610,10 +607,10 @@ class Parser():
610 607 """
611 608 try:
612 609 data = self.data_image[str(0x0010)][str(0x2150)]
613   - except(KeyError):
  610 + except (KeyError):
614 611 return ""
615 612  
616   - if (data):
  613 + if data:
617 614 return data
618 615 return ""
619 616  
... ... @@ -627,10 +624,10 @@ class Parser():
627 624 """
628 625 try:
629 626 data = self.data_image[str(0x0010)][str(0x2152)]
630   - except(KeyError):
  627 + except (KeyError):
631 628 return ""
632 629  
633   - if (data):
  630 + if data:
634 631 return data
635 632 return ""
636 633  
... ... @@ -643,10 +640,10 @@ class Parser():
643 640 """
644 641 try:
645 642 data = self.data_image[str(0x0010)][str(0x2154)]
646   - except(KeyError):
  643 + except (KeyError):
647 644 return ""
648 645  
649   - if (data):
  646 + if data:
650 647 return data
651 648 return ""
652 649  
... ... @@ -660,10 +657,10 @@ class Parser():
660 657 """
661 658 try:
662 659 data = self.data_image[str(0x0010)][str(0x2297)]
663   - except(KeyError):
  660 + except (KeyError):
664 661 return ""
665 662  
666   - if (data):
  663 + if data:
667 664 return data
668 665 return ""
669 666  
... ... @@ -676,11 +673,11 @@ class Parser():
676 673 DICOM standard tag (0x0010, 0x2298) was used.
677 674 """
678 675 try:
679   - data = self.data_image[str(0x0010)][str(0x2298)]
680   - except(KeyError):
  676 + data = self.data_image[str(0x0010)][str(0x2298)]
  677 + except (KeyError):
681 678 return ""
682 679  
683   - if (data):
  680 + if data:
684 681 return data
685 682 return ""
686 683  
... ... @@ -694,10 +691,10 @@ class Parser():
694 691 """
695 692 try:
696 693 data = self.data_image[str(0x0010)][str(0x2299)]
697   - except(KeyError):
  694 + except (KeyError):
698 695 return ""
699 696  
700   - if (data):
  697 + if data:
701 698 return data
702 699 return ""
703 700  
... ... @@ -711,10 +708,10 @@ class Parser():
711 708 """
712 709 try:
713 710 data = self.data_image[str(0x0010)][str(0x2000)]
714   - except(KeyError):
  711 + except (KeyError):
715 712 return ""
716 713  
717   - if (data):
  714 + if data:
718 715 return data
719 716 return ""
720 717  
... ... @@ -727,15 +724,14 @@ class Parser():
727 724 DICOM standard tag (0x0008, 0x2110) was used.
728 725 """
729 726 try:
730   - data = self.data_image[str(0x0008)][str(0x2110)]
731   - except(KeyError):
  727 + data = self.data_image[str(0x0008)][str(0x2110)]
  728 + except (KeyError):
732 729 return ""
733 730  
734   - if (data):
  731 + if data:
735 732 return data
736 733 return ""
737 734  
738   -
739 735 def GetPhysicianReferringName(self):
740 736 """
741 737 Return string containing physician
... ... @@ -746,16 +742,15 @@ class Parser():
746 742 """
747 743 try:
748 744 data = self.data_image[str(0x0008)][str(0x0090)]
749   - except(KeyError):
  745 + except (KeyError):
750 746 return ""
751 747  
752 748 if data == "None":
753 749 return ""
754   - if (data):
  750 + if data:
755 751 return data
756 752 return ""
757 753  
758   -
759 754 def GetPhysicianReferringAddress(self):
760 755 """
761 756 Return string containing physician's address.
... ... @@ -765,10 +760,10 @@ class Parser():
765 760 """
766 761 try:
767 762 data = self.data_image[str(0x0008)][str(0x0092)]
768   - except(KeyError):
  763 + except (KeyError):
769 764 return ""
770 765  
771   - if (data):
  766 + if data:
772 767 return data
773 768 return ""
774 769  
... ... @@ -781,10 +776,10 @@ class Parser():
781 776 """
782 777 try:
783 778 data = self.data_image[str(0x0008)][str(0x0094)]
784   - except(KeyError):
  779 + except (KeyError):
785 780 return ""
786   -
787   - if (data):
  781 +
  782 + if data:
788 783 return data
789 784 return ""
790 785  
... ... @@ -797,10 +792,10 @@ class Parser():
797 792 """
798 793 try:
799 794 data = self.data_image[str(0x0018)][str(0x1030)]
800   - except(KeyError):
  795 + except (KeyError):
801 796 return None
802 797  
803   - if (data):
  798 + if data:
804 799 return data
805 800 return None
806 801  
... ... @@ -815,17 +810,17 @@ class Parser():
815 810 """
816 811 try:
817 812 data = self.data_image[str(0x008)][str(0x008)]
818   - except(IndexError):
  813 + except (IndexError):
819 814 return []
820 815 # TODO: Check if set image type to empty is the right way of handling
821 816 # the cases where there is not this tag.
822 817 except KeyError:
823 818 return []
824 819  
825   - if (data):
  820 + if data:
826 821 try:
827   - return data.split('\\')
828   - except(IndexError):
  822 + return data.split("\\")
  823 + except (IndexError):
829 824 return []
830 825 return []
831 826  
... ... @@ -839,10 +834,10 @@ class Parser():
839 834 """
840 835 try:
841 836 data = self.data_image[str(0x0008)][str(0x0016)]
842   - except(KeyError):
  837 + except (KeyError):
843 838 return ""
844 839  
845   - if (data):
  840 + if data:
846 841 return data
847 842 return ""
848 843  
... ... @@ -856,10 +851,10 @@ class Parser():
856 851 """
857 852 try:
858 853 data = self.data_image[str(0x0008)][str(0x0018)]
859   - except(KeyError):
  854 + except (KeyError):
860 855 return ""
861 856  
862   - if (data):
  857 + if data:
863 858 return data
864 859 return ""
865 860  
... ... @@ -872,11 +867,11 @@ class Parser():
872 867 Critical DICOM Tag (0x0020,0x000D). Cannot be edited.
873 868 """
874 869 try:
875   - data = self.data_image[str(0x0020)][str(0x000D)]
876   - except(KeyError):
  870 + data = self.data_image[str(0x0020)][str(0x000D)]
  871 + except (KeyError):
877 872 return ""
878 873  
879   - if (data):
  874 + if data:
880 875 return data
881 876 return ""
882 877  
... ... @@ -893,11 +888,11 @@ class Parser():
893 888 """
894 889 try:
895 890 data = self.data_image[str(0x0020)][str(0x0037)].replace(",", ".")
896   - except(KeyError):
  891 + except (KeyError):
897 892 return [1.0, 0.0, 0.0, 0.0, 1.0, 0.0]
898 893  
899   - if (data):
900   - return [float(value) for value in data.split('\\')]
  894 + if data:
  895 + return [float(value) for value in data.split("\\")]
901 896 return [1.0, 0.0, 0.0, 0.0, 1.0, 0.0]
902 897  
903 898 def GetImageColumnOrientation(self):
... ... @@ -911,11 +906,11 @@ class Parser():
911 906 """
912 907 try:
913 908 data = self.data_image[str(0x0020)][str(0x0037)]
914   - except(KeyError):
  909 + except (KeyError):
915 910 return [0.0, 1.0, 0.0]
916 911  
917   - if (data):
918   - return [float(value) for value in data.split('\\')[3:6]]
  912 + if data:
  913 + return [float(value) for value in data.split("\\")[3:6]]
919 914 return [0.0, 1.0, 0.0]
920 915  
921 916 def GetImageRowOrientation(self):
... ... @@ -929,11 +924,11 @@ class Parser():
929 924 """
930 925 try:
931 926 data = self.data_image[str(0x0020)][str(0x0037)]
932   - except(KeyError):
  927 + except (KeyError):
933 928 return [1.0, 0.0, 0.0]
934 929  
935   - if (data):
936   - return [float(value) for value in data.split('\\')[0:3]]
  930 + if data:
  931 + return [float(value) for value in data.split("\\")[0:3]]
937 932 return [1.0, 0.0, 0.0]
938 933  
939 934 def GetFrameReferenceUID(self):
... ... @@ -945,10 +940,10 @@ class Parser():
945 940 """
946 941 try:
947 942 data = self.data_image[str(0x0020)][str(0x0052)]
948   - except(KeyError):
  943 + except (KeyError):
949 944 return ""
950 945  
951   - if (data):
  946 + if data:
952 947 return data
953 948 return ""
954 949  
... ... @@ -980,7 +975,7 @@ class Parser():
980 975 sf = gdcm.StringFilter()
981 976 sf.SetFile(self.gdcm_reader.GetFile())
982 977 res = sf.ToStringPair(tag)
983   - if (res[1]):
  978 + if res[1]:
984 979 return res[1]
985 980 return ""
986 981  
... ... @@ -996,7 +991,7 @@ class Parser():
996 991 sf = gdcm.StringFilter()
997 992 sf.SetFile(self.gdcm_reader.GetFile())
998 993 res = sf.ToStringPair(tag)
999   - if (res[1]):
  994 + if res[1]:
1000 995 return int(res[1])
1001 996 return ""
1002 997  
... ... @@ -1011,7 +1006,7 @@ class Parser():
1011 1006 sf = gdcm.StringFilter()
1012 1007 sf.SetFile(self.gdcm_reader.GetFile())
1013 1008 res = sf.ToStringPair(tag)
1014   - if (res[1]):
  1009 + if res[1]:
1015 1010 return int(res[1])
1016 1011 return ""
1017 1012  
... ... @@ -1026,9 +1021,9 @@ class Parser():
1026 1021 """
1027 1022 try:
1028 1023 data = self.data_image[str(0x0018)][str(0x1030)]
1029   - if (data):
  1024 + if data:
1030 1025 return data
1031   - except(KeyError):
  1026 + except (KeyError):
1032 1027 return ""
1033 1028 return ""
1034 1029  
... ... @@ -1050,10 +1045,10 @@ class Parser():
1050 1045 """
1051 1046 try:
1052 1047 data = self.data_image[str(0x0018)][str(0x0020)]
1053   - except(KeyError):
  1048 + except (KeyError):
1054 1049 return ""
1055 1050  
1056   - if (data):
  1051 + if data:
1057 1052 return data
1058 1053 return ""
1059 1054  
... ... @@ -1065,12 +1060,12 @@ class Parser():
1065 1060 DICOM standard tag (0x0008, 0x0080) was used.
1066 1061 """
1067 1062 try:
1068   - data = self.data_image[str(0x0008)][str(0x0080)]
1069   - except(KeyError):
  1063 + data = self.data_image[str(0x0008)][str(0x0080)]
  1064 + except (KeyError):
1070 1065 return ""
1071 1066  
1072   - if (data):
1073   - return data
  1067 + if data:
  1068 + return data
1074 1069 return ""
1075 1070  
1076 1071 def GetInstitutionAddress(self):
... ... @@ -1084,10 +1079,10 @@ class Parser():
1084 1079 """
1085 1080 try:
1086 1081 data = self.data_image[str(0x0008)][str(0x0081)]
1087   - except(KeyError):
  1082 + except (KeyError):
1088 1083 return ""
1089 1084  
1090   - if (data):
  1085 + if data:
1091 1086 return data
1092 1087 return ""
1093 1088  
... ... @@ -1101,10 +1096,10 @@ class Parser():
1101 1096 """
1102 1097 try:
1103 1098 data = self.data_image[str(0x0020)][str(0x000D)]
1104   - except(KeyError):
  1099 + except (KeyError):
1105 1100 return ""
1106 1101  
1107   - if (data):
  1102 + if data:
1108 1103 return data
1109 1104 return ""
1110 1105  
... ... @@ -1117,10 +1112,10 @@ class Parser():
1117 1112 """
1118 1113 try:
1119 1114 data = self.data_image[str(0x0010)][str(0x2180)]
1120   - except(KeyError):
  1115 + except (KeyError):
1121 1116 return ""
1122 1117  
1123   - if (data):
  1118 + if data:
1124 1119 return data
1125 1120 return ""
1126 1121  
... ... @@ -1137,7 +1132,7 @@ class Parser():
1137 1132 sf = gdcm.StringFilter()
1138 1133 sf.SetFile(self.gdcm_reader.GetFile())
1139 1134 res = sf.ToStringPair(tag)
1140   - if (res[1]):
  1135 + if res[1]:
1141 1136 return int(res[1])
1142 1137 return ""
1143 1138  
... ... @@ -1149,16 +1144,16 @@ class Parser():
1149 1144  
1150 1145 DICOM standard tag (0x0028, 0x0100) was used.
1151 1146 """
1152   - #tag = gdcm.Tag(0x0028, 0x0100)
1153   - #sf = gdcm.StringFilter()
1154   - #sf.SetFile(self.gdcm_reader.GetFile())
1155   - #res = sf.ToStringPair(tag)
  1147 + # tag = gdcm.Tag(0x0028, 0x0100)
  1148 + # sf = gdcm.StringFilter()
  1149 + # sf.SetFile(self.gdcm_reader.GetFile())
  1150 + # res = sf.ToStringPair(tag)
1156 1151 try:
1157 1152 data = self.data_image[str(0x0028)][str(0x0100)]
1158   - except(KeyError):
  1153 + except (KeyError):
1159 1154 return ""
1160 1155  
1161   - if (data):
  1156 + if data:
1162 1157 return int(data)
1163 1158 return ""
1164 1159  
... ... @@ -1174,7 +1169,6 @@ class Parser():
1174 1169 return 1
1175 1170 return int(data)
1176 1171  
1177   -
1178 1172 def GetPatientBirthDate(self):
1179 1173 """
1180 1174 Return string containing the patient's birth date using the
... ... @@ -1186,14 +1180,13 @@ class Parser():
1186 1180 # TODO: internationalize data
1187 1181 try:
1188 1182 data = self.data_image[str(0x0010)][str(0x0030)]
1189   - except(KeyError):
  1183 + except (KeyError):
1190 1184 return ""
1191 1185  
1192   - if (data) and (data != 'None'):
  1186 + if (data) and (data != "None"):
1193 1187 return self.__format_date(str(data))
1194 1188 return ""
1195 1189  
1196   -
1197 1190 def GetStudyID(self):
1198 1191 """
1199 1192 Return string containing the Study ID.
... ... @@ -1203,13 +1196,13 @@ class Parser():
1203 1196 """
1204 1197 try:
1205 1198 data = self.data_image[str(0x0020)][str(0x0010)]
1206   - except(KeyError):
  1199 + except (KeyError):
1207 1200 return ""
1208 1201  
1209   - if (data):
  1202 + if data:
1210 1203 return str(data)
1211 1204 return ""
1212   -
  1205 +
1213 1206 def GetAcquisitionGantryTilt(self):
1214 1207 """
1215 1208 Return floating point containing nominal angle of
... ... @@ -1220,10 +1213,10 @@ class Parser():
1220 1213 """
1221 1214 try:
1222 1215 data = self.data_image[str(0x0018)][str(0x1120)]
1223   - except(KeyError):
  1216 + except (KeyError):
1224 1217 return 0.0
1225 1218  
1226   - if (data):
  1219 + if data:
1227 1220 return float(str(data))
1228 1221 return 0.0
1229 1222  
... ... @@ -1239,16 +1232,16 @@ class Parser():
1239 1232 """
1240 1233 try:
1241 1234 data = self.data_image[str(0x0010)][str(0x0040)]
1242   - except(KeyError):
  1235 + except (KeyError):
1243 1236 return ""
1244 1237  
1245   - if (data):
  1238 + if data:
1246 1239 name = data.strip()
1247 1240 encoding = self.GetEncoding()
1248 1241 try:
1249 1242 # Returns a unicode decoded in the own dicom encoding
1250   - return utils.decode(name, encoding, 'replace')
1251   - except(UnicodeEncodeError):
  1243 + return utils.decode(name, encoding, "replace")
  1244 + except (UnicodeEncodeError):
1252 1245 return name
1253 1246  
1254 1247 return ""
... ... @@ -1263,11 +1256,11 @@ class Parser():
1263 1256 """
1264 1257 try:
1265 1258 data = self.data_image[str(0x0010)][str(0x1010)]
1266   - except(KeyError):
  1259 + except (KeyError):
1267 1260 return ""
1268 1261  
1269   - if (data):
1270   - age = (data.split('Y')[0])
  1262 + if data:
  1263 + age = data.split("Y")[0]
1271 1264 try:
1272 1265 return int(age)
1273 1266 except ValueError:
... ... @@ -1283,7 +1276,7 @@ class Parser():
1283 1276 """
1284 1277 try:
1285 1278 data = self.data_image[str(0x0010)][str(0x0010)]
1286   - except(KeyError):
  1279 + except (KeyError):
1287 1280 return ""
1288 1281  
1289 1282 encoding = self.GetEncoding()
... ... @@ -1303,19 +1296,18 @@ class Parser():
1303 1296 """
1304 1297 try:
1305 1298 data = self.data_image[str(0x0010)][str(0x0020)]
1306   - except(KeyError):
  1299 + except (KeyError):
1307 1300 return ""
1308 1301  
1309   - if (data):
  1302 + if data:
1310 1303 encoding = self.GetEncoding()
1311 1304 # Returns a unicode decoded in the own dicom encoding
1312 1305 try:
1313   - return utils.decode(data, encoding, 'replace')
1314   - except(UnicodeEncodeError):
  1306 + return utils.decode(data, encoding, "replace")
  1307 + except (UnicodeEncodeError):
1315 1308 return data
1316 1309 return ""
1317 1310  
1318   -
1319 1311 def GetEquipmentXRayTubeCurrent(self):
1320 1312 """
1321 1313 Return float value associated to the X-ray tube current
... ... @@ -1326,10 +1318,10 @@ class Parser():
1326 1318 """
1327 1319 try:
1328 1320 data = self.data_image[str(0x0018)][str(0x1151)]
1329   - except(KeyError):
  1321 + except (KeyError):
1330 1322 return ""
1331 1323  
1332   - if (data):
  1324 + if data:
1333 1325 return data
1334 1326 return ""
1335 1327  
... ... @@ -1343,10 +1335,10 @@ class Parser():
1343 1335 """
1344 1336 try:
1345 1337 data = self.data_image[str(0x0018)][str(0x1152)]
1346   - except(KeyError):
  1338 + except (KeyError):
1347 1339 return ""
1348 1340  
1349   - if (data):
  1341 + if data:
1350 1342 return float(data)
1351 1343 return ""
1352 1344  
... ... @@ -1360,10 +1352,10 @@ class Parser():
1360 1352 """
1361 1353 try:
1362 1354 data = self.data_image[str(0x0018)][str(0x0060)]
1363   - except(KeyError):
  1355 + except (KeyError):
1364 1356 return ""
1365 1357  
1366   - if (data):
  1358 + if data:
1367 1359 return float(data)
1368 1360 return ""
1369 1361  
... ... @@ -1377,9 +1369,9 @@ class Parser():
1377 1369 """
1378 1370 try:
1379 1371 data = self.data_image[str(0x0018)][str(0x0050)].replace(",", ".")
1380   - except(KeyError):
  1372 + except (KeyError):
1381 1373 return 0
1382   - if (data):
  1374 + if data:
1383 1375 return float(data)
1384 1376 return 0
1385 1377  
... ... @@ -1395,10 +1387,10 @@ class Parser():
1395 1387 """
1396 1388 try:
1397 1389 data = self.data_image[str(0x0018)][str(0x1210)]
1398   - except(KeyError):
  1390 + except (KeyError):
1399 1391 return ""
1400 1392  
1401   - if (data):
  1393 + if data:
1402 1394 return data
1403 1395 return ""
1404 1396  
... ... @@ -1412,10 +1404,10 @@ class Parser():
1412 1404 """
1413 1405 try:
1414 1406 data = self.data_image[str(0x0008)][str(0x0080)]
1415   - except(KeyError):
  1407 + except (KeyError):
1416 1408 return ""
1417 1409  
1418   - if (data):
  1410 + if data:
1419 1411 return data
1420 1412 return ""
1421 1413  
... ... @@ -1429,10 +1421,10 @@ class Parser():
1429 1421 """
1430 1422 try:
1431 1423 data = self.data_image[str(0x0008)][str(0x1010)]
1432   - except(KeyError):
  1424 + except (KeyError):
1433 1425 return ""
1434 1426  
1435   - if (data):
  1427 + if data:
1436 1428 return data
1437 1429 return ""
1438 1430  
... ... @@ -1446,24 +1438,24 @@ class Parser():
1446 1438 """
1447 1439 try:
1448 1440 data = self.data_image[str(0x0008)][str(0x1090)]
1449   - except(KeyError):
  1441 + except (KeyError):
1450 1442 return ""
1451 1443  
1452   - if (data):
  1444 + if data:
1453 1445 return data
1454 1446 return ""
1455 1447  
1456 1448 def GetManufacturerName(self):
1457 1449 """
1458   - Return Manufacturer of the equipment that produced
  1450 + Return Manufacturer of the equipment that produced
1459 1451 the composite instances.
1460 1452 """
1461 1453 try:
1462 1454 data = self.data_image[str(0x0008)][str(0x0070)]
1463   - except(KeyError):
  1455 + except (KeyError):
1464 1456 return ""
1465 1457  
1466   - if (data):
  1458 + if data:
1467 1459 return data
1468 1460 return ""
1469 1461  
... ... @@ -1476,10 +1468,10 @@ class Parser():
1476 1468 """
1477 1469 try:
1478 1470 data = self.data_image[str(0x0008)][str(0x1010)]
1479   - except(KeyError):
  1471 + except (KeyError):
1480 1472 return ""
1481 1473  
1482   - if (data):
  1474 + if data:
1483 1475 return data
1484 1476 return ""
1485 1477  
... ... @@ -1494,14 +1486,13 @@ class Parser():
1494 1486 """
1495 1487 try:
1496 1488 data = self.data_image[str(0x0008)][str(0x0060)]
1497   - except(KeyError):
  1489 + except (KeyError):
1498 1490 return ""
1499 1491  
1500   - if (data):
  1492 + if data:
1501 1493 return data
1502 1494 return ""
1503 1495  
1504   -
1505 1496 def GetImageNumber(self):
1506 1497 """
1507 1498 Return slice number (integer).
... ... @@ -1511,10 +1502,10 @@ class Parser():
1511 1502 """
1512 1503 try:
1513 1504 data = self.data_image[str(0x0020)][str(0x0013)]
1514   - except(KeyError):
  1505 + except (KeyError):
1515 1506 return 0
1516 1507  
1517   - if (data):
  1508 + if data:
1518 1509 return int(data)
1519 1510 return 0
1520 1511  
... ... @@ -1527,10 +1518,10 @@ class Parser():
1527 1518 """
1528 1519 try:
1529 1520 data = self.data_image[str(0x0008)][str(0x1030)]
1530   - if (data):
  1521 + if data:
1531 1522 encoding = self.GetEncoding()
1532   - return utils.decode(data, encoding, 'replace')
1533   - except(KeyError):
  1523 + return utils.decode(data, encoding, "replace")
  1524 + except (KeyError):
1534 1525 return ""
1535 1526  
1536 1527 def GetStudyAdmittingDiagnosis(self):
... ... @@ -1546,11 +1537,10 @@ class Parser():
1546 1537 sf.SetFile(self.gdcm_reader.GetFile())
1547 1538 res = sf.ToStringPair(tag)
1548 1539  
1549   - if (res[1]):
  1540 + if res[1]:
1550 1541 return str(res[1])
1551 1542 return ""
1552 1543  
1553   -
1554 1544 def GetSeriesDescription(self):
1555 1545 """
1556 1546 Return a string with a description of the series.
... ... @@ -1558,7 +1548,7 @@ class Parser():
1558 1548 """
1559 1549 try:
1560 1550 data = self.data_image[str(0x0008)][str(0x103E)]
1561   - except(KeyError):
  1551 + except (KeyError):
1562 1552 return _("unnamed")
1563 1553  
1564 1554 encoding = self.GetEncoding()
... ... @@ -1581,11 +1571,11 @@ class Parser():
1581 1571 """
1582 1572 try:
1583 1573 data = self.data_image[str(0x0008)][str(0x0033)]
1584   - except(KeyError):
  1574 + except (KeyError):
1585 1575 return ""
1586 1576  
1587   - if (data) and (data != 'None'):
1588   - return self.__format_time(data)
  1577 + if (data) and (data != "None"):
  1578 + return self.__format_time(data)
1589 1579 return ""
1590 1580  
1591 1581 def GetAcquisitionTime(self):
... ... @@ -1595,10 +1585,10 @@ class Parser():
1595 1585 """
1596 1586 try:
1597 1587 data = self.data_image[str(0x0008)][str(0x0032)]
1598   - except(KeyError):
  1588 + except (KeyError):
1599 1589 return ""
1600 1590  
1601   - if (data):
  1591 + if data:
1602 1592 return self.__format_time(data)
1603 1593 return ""
1604 1594  
... ... @@ -1609,10 +1599,10 @@ class Parser():
1609 1599 """
1610 1600 try:
1611 1601 data = self.data_image[str(0x0020)][str(0x0011)]
1612   - except(KeyError):
  1602 + except (KeyError):
1613 1603 return ""
1614   -
1615   - if (data):
  1604 +
  1605 + if data:
1616 1606 return data
1617 1607 return ""
1618 1608  
... ... @@ -1624,8 +1614,8 @@ class Parser():
1624 1614 try:
1625 1615 encoding_value = self.data_image[str(0x0008)][str(0x0005)]
1626 1616 return const.DICOM_ENCODING_TO_PYTHON[encoding_value]
1627   - except(KeyError):
1628   - return 'ISO_IR_100'
  1617 + except (KeyError):
  1618 + return "ISO_IR_100"
1629 1619  
1630 1620  
1631 1621 class DicomWriter:
... ... @@ -1665,7 +1655,6 @@ class DicomWriter:
1665 1655 self.new_dicom = vtkgdcm.vtkGDCMImageWriter()
1666 1656 reader = self.reader = gdcm.Reader()
1667 1657  
1668   -
1669 1658 def SetFileName(self, path):
1670 1659 """
1671 1660 Set Dicom File Name
... ... @@ -1674,19 +1663,16 @@ class DicomWriter:
1674 1663  
1675 1664 self.reader.SetFileName(path)
1676 1665  
1677   - if (self.reader.Read()):
  1666 + if self.reader.Read():
1678 1667  
1679 1668 self.anony.SetFile(self.reader.GetFile())
1680 1669  
1681   -
1682   -
1683 1670 def SetInput(self, img_data):
1684 1671 """
1685 1672 Input vtkImageData
1686 1673 """
1687 1674 self.img_data = img_data
1688 1675  
1689   -
1690 1676 def __CreateNewDicom(self, img_data):
1691 1677 """
1692 1678 Create New Dicom File, input is
... ... @@ -1697,7 +1683,6 @@ class DicomWriter:
1697 1683 new_dicom.SetInput(img_data)
1698 1684 new_dicom.Write()
1699 1685  
1700   -
1701 1686 def SaveIsNew(self, img_data):
1702 1687 """
1703 1688 Write Changes in Dicom file or Create
... ... @@ -1706,12 +1691,11 @@ class DicomWriter:
1706 1691  
1707 1692 self.__CreateNewDicom(img_data)
1708 1693  
1709   - #Is necessary to create and add
1710   - #information in the dicom tag
  1694 + # Is necessary to create and add
  1695 + # information in the dicom tag
1711 1696 self.SetFileName(self.path)
1712 1697 self.anony.SetFile(self.reader.GetFile())
1713 1698  
1714   -
1715 1699 def Save(self):
1716 1700  
1717 1701 reader = self.reader
... ... @@ -1721,84 +1705,63 @@ class DicomWriter:
1721 1705 writer.SetFileName(self.path)
1722 1706 writer.Write()
1723 1707  
1724   -
1725 1708 def SetPatientName(self, patient):
1726 1709 """
1727 1710 Set Patient Name requeries string type
1728 1711 """
1729   - self.anony.Replace(gdcm.Tag(0x0010,0x0010), \
1730   - str(patient))
1731   -
  1712 + self.anony.Replace(gdcm.Tag(0x0010, 0x0010), str(patient))
1732 1713  
1733 1714 def SetImageThickness(self, thickness):
1734 1715 """
1735 1716 Set thickness value requeries float type
1736 1717 """
1737   - self.anony.Replace(gdcm.Tag(0x0018,0x0050), \
1738   - str(thickness))
1739   -
  1718 + self.anony.Replace(gdcm.Tag(0x0018, 0x0050), str(thickness))
1740 1719  
1741 1720 def SetImageSeriesNumber(self, number):
1742 1721 """
1743 1722 Set Serie Number value requeries int type
1744 1723 """
1745   - self.anony.Replace(gdcm.Tag(0x0020,0x0011), \
1746   - str(number))
1747   -
  1724 + self.anony.Replace(gdcm.Tag(0x0020, 0x0011), str(number))
1748 1725  
1749 1726 def SetImageNumber(self, number):
1750 1727 """
1751 1728 Set image Number value requeries int type
1752 1729 """
1753   - self.anony.Replace(gdcm.Tag(0x0020,0x0013),
1754   - str(number))
1755   -
  1730 + self.anony.Replace(gdcm.Tag(0x0020, 0x0013), str(number))
1756 1731  
1757 1732 def SetImageLocation(self, location):
1758 1733 """
1759 1734 Set slice location value requeries float type
1760 1735 """
1761   - self.anony.Replace(gdcm.Tag(0x0020,0x1041),\
1762   - str(number))
1763   -
  1736 + self.anony.Replace(gdcm.Tag(0x0020, 0x1041), str(number))
1764 1737  
1765 1738 def SetImagePosition(self, position):
1766 1739 """
1767 1740 Set slice position value requeries list
1768 1741 with three values x, y and z
1769 1742 """
1770   - self.anony.Replace(gdcm.Tag(0x0020,0x0032), \
1771   - str(position[0]) + \
1772   - "\\" + str(position[1]) + \
1773   - "\\" + str(position[2]))
1774   -
  1743 + self.anony.Replace(
  1744 + gdcm.Tag(0x0020, 0x0032),
  1745 + str(position[0]) + "\\" + str(position[1]) + "\\" + str(position[2]),
  1746 + )
1775 1747  
1776 1748 def SetAcquisitionModality(self, modality):
1777 1749 """
1778 1750 Set modality study CT or RM
1779 1751 """
1780   - self.anony.Replace(gdcm.Tag(0x0008,0x0060), \
1781   - str(modality))
1782   -
  1752 + self.anony.Replace(gdcm.Tag(0x0008, 0x0060), str(modality))
1783 1753  
1784 1754 def SetPixelSpacing(self, spacing):
1785 1755 """
1786 1756 Set pixel spacing x and y
1787 1757 """
1788   - self.anony.Replace(gdcm.Tag(0x0028,0x0030), \
1789   - str(spacing))
1790   -
  1758 + self.anony.Replace(gdcm.Tag(0x0028, 0x0030), str(spacing))
1791 1759  
1792 1760 def SetInstitutionName(self, institution):
1793 1761 """
1794 1762 Set institution name
1795 1763 """
1796   - self.anony.Replace(gdcm.Tag(0x0008, 0x0080), \
1797   - str(institution))
1798   -
1799   -
1800   -
1801   -
  1764 + self.anony.Replace(gdcm.Tag(0x0008, 0x0080), str(institution))
1802 1765  
1803 1766  
1804 1767 def BuildDictionary(filename):
... ... @@ -1816,10 +1779,11 @@ def BuildDictionary(filename):
1816 1779 # file, given keys in info_keys list. Example:
1817 1780 # info["AcquisitionDate"] = dicom.GetAcquisitionDate()
1818 1781 for key in INFO_KEYS:
1819   - info[key] = eval("parser.Get"+key+"()")
  1782 + info[key] = eval("parser.Get" + key + "()")
1820 1783  
1821 1784 return info
1822 1785  
  1786 +
1823 1787 def LoadDictionary(filename):
1824 1788 """
1825 1789 Given a binary file (containing a dictionary), return dictionary
... ... @@ -1844,14 +1808,15 @@ def DumpDictionary(filename, dictionary=info):
1844 1808 pickle.dump(info, fp)
1845 1809 fp.close()
1846 1810  
  1811 +
1847 1812 if __name__ == "__main__":
1848 1813  
1849 1814 # Example of how to use Parser
1850 1815 fail_count = 0
1851 1816 total = 48
1852 1817  
1853   - for i in range(1,total+1):
1854   - filename = "..//data//"+str(i)+".dcm"
  1818 + for i in range(1, total + 1):
  1819 + filename = "..//data//" + str(i) + ".dcm"
1855 1820  
1856 1821 parser = Parser()
1857 1822 if parser.SetFileName(filename):
... ... @@ -1865,8 +1830,8 @@ if __name__ == &quot;__main__&quot;:
1865 1830 print("z:", parser.GetDimensionZ())
1866 1831 else:
1867 1832 print("--------------------------------------------------")
1868   - total-=1
1869   - fail_count+=1
  1833 + total -= 1
  1834 + fail_count += 1
1870 1835  
1871 1836 print("\nREPORT:")
1872 1837 print("failed: ", fail_count)
... ... @@ -1874,16 +1839,13 @@ if __name__ == &quot;__main__&quot;:
1874 1839  
1875 1840 # Example of how to use auxiliary functions
1876 1841 total = 38
1877   - for i in range(1,total+1):
1878   - if (i==8) or (i==9) or (i==13):
  1842 + for i in range(1, total + 1):
  1843 + if (i == 8) or (i == 9) or (i == 13):
1879 1844 pass
1880 1845 else:
1881   - filename = "..//data//"+str(i)+".dcm"
  1846 + filename = "..//data//" + str(i) + ".dcm"
1882 1847 info = BuildDictionary(filename)
1883   - #print info
1884   -
1885   -
1886   -
  1848 + # print info
1887 1849  
1888 1850  
1889 1851 class Dicom(object):
... ... @@ -1896,7 +1858,7 @@ class Dicom(object):
1896 1858 self.LoadImageInfo()
1897 1859 self.LoadPatientInfo()
1898 1860 self.LoadAcquisitionInfo()
1899   - #self.LoadStudyInfo()
  1861 + # self.LoadStudyInfo()
1900 1862  
1901 1863 def LoadImageInfo(self):
1902 1864 self.image = Image()
... ... @@ -1911,9 +1873,6 @@ class Dicom(object):
1911 1873 self.acquisition.SetParser(self.parser)
1912 1874  
1913 1875  
1914   -
1915   -
1916   -
1917 1876 class Patient(object):
1918 1877 def __init__(self):
1919 1878 pass
... ... @@ -1928,7 +1887,6 @@ class Patient(object):
1928 1887  
1929 1888  
1930 1889 class Acquisition(object):
1931   -
1932 1890 def __init__(self):
1933 1891 pass
1934 1892  
... ... @@ -1950,7 +1908,6 @@ class Acquisition(object):
1950 1908  
1951 1909  
1952 1910 class Image(object):
1953   -
1954 1911 def __init__(self):
1955 1912 pass
1956 1913  
... ... @@ -1969,14 +1926,14 @@ class Image(object):
1969 1926 self.time = parser.GetImageTime()
1970 1927 self.type = parser.GetImageType()
1971 1928 self.size = (parser.GetDimensionX(), parser.GetDimensionY())
1972   - #self.imagedata = parser.GetImageData()
  1929 + # self.imagedata = parser.GetImageData()
1973 1930 self.bits_allocad = parser._GetBitsAllocated()
1974 1931 self.thumbnail_path = parser.thumbnail_path
1975 1932  
1976 1933 self.number_of_frames = parser.GetNumberOfFrames()
1977 1934 self.samples_per_pixel = parser.GetImageSamplesPerPixel()
1978 1935  
1979   - if (parser.GetImageThickness()):
  1936 + if parser.GetImageThickness():
1980 1937 self.spacing.append(parser.GetImageThickness())
1981 1938 else:
1982 1939 self.spacing.append(1.0)
... ...
invesalius/reader/dicom_reader.py
  Diff comments   View file @7f99565
1   -#--------------------------------------------------------------------------
  1 +# --------------------------------------------------------------------------
2 2 # Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
3 3 # Copyright: (C) 2001 Centro de Pesquisas Renato Archer
4 4 # Homepage: http://www.softwarepublico.gov.br
5 5 # Contact: invesalius@cti.gov.br
6 6 # License: GNU - GPL 2 (LICENSE.txt/LICENCA.txt)
7   -#--------------------------------------------------------------------------
  7 +# --------------------------------------------------------------------------
8 8 # Este programa e software livre; voce pode redistribui-lo e/ou
9 9 # modifica-lo sob os termos da Licenca Publica Geral GNU, conforme
10 10 # publicada pela Free Software Foundation; de acordo com a versao 2
... ... @@ -15,36 +15,35 @@
15 15 # COMERCIALIZACAO ou de ADEQUACAO A QUALQUER PROPOSITO EM
16 16 # PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
17 17 # detalhes.
18   -#--------------------------------------------------------------------------
  18 +# --------------------------------------------------------------------------
19 19 import os
20   -import threading
21   -import tempfile
22 20 import sys
23   -
  21 +import tempfile
  22 +import threading
24 23 from multiprocessing import cpu_count
25 24  
26   -import vtk
27 25 import gdcm
  26 +import vtk
  27 +
28 28 # Not showing GDCM warning and debug messages
29 29 gdcm.Trace_DebugOff()
30 30 gdcm.Trace_WarningOff()
31   -from invesalius.pubsub import pub as Publisher
  31 +import glob
  32 +import plistlib
32 33  
33 34 import invesalius.constants as const
34 35 import invesalius.reader.dicom as dicom
35 36 import invesalius.reader.dicom_grouper as dicom_grouper
36 37 import invesalius.session as session
37   -import glob
38 38 import invesalius.utils as utils
39   -
40 39 from invesalius import inv_paths
41 40 from invesalius.data import imagedata_utils
  41 +from invesalius.pubsub import pub as Publisher
42 42  
43   -import plistlib
44   -
45   -if sys.platform == 'win32':
  43 +if sys.platform == "win32":
46 44 try:
47 45 import win32api
  46 +
48 47 _has_win32api = True
49 48 except ImportError:
50 49 _has_win32api = False
... ... @@ -79,6 +78,7 @@ def SelectLargerDicomGroup(patient_group):
79 78  
80 79 return larger_group
81 80  
  81 +
82 82 def SortFiles(filelist, dicom):
83 83 # Sort slices
84 84 # FIXME: Coronal Crash. necessary verify
... ... @@ -89,15 +89,17 @@ def SortFiles(filelist, dicom):
89 89 sorter.SetZSpacingTolerance(1e-10)
90 90 sorter.Sort(filelist)
91 91  
92   - #Getting organized image
  92 + # Getting organized image
93 93 filelist = sorter.GetFilenames()
94 94  
95 95 return filelist
96 96  
  97 +
97 98 tag_labels = {}
98 99 main_dict = {}
99 100 dict_file = {}
100 101  
  102 +
101 103 class LoadDicom:
102 104 def __init__(self, grouper, filepath):
103 105 self.grouper = grouper
... ... @@ -109,8 +111,11 @@ class LoadDicom:
109 111 reader = gdcm.ImageReader()
110 112 if _has_win32api:
111 113 try:
112   - reader.SetFileName(utils.encode(win32api.GetShortPathName(self.filepath),
113   - const.FS_ENCODE))
  114 + reader.SetFileName(
  115 + utils.encode(
  116 + win32api.GetShortPathName(self.filepath), const.FS_ENCODE
  117 + )
  118 + )
114 119 except TypeError:
115 120 reader.SetFileName(win32api.GetShortPathName(self.filepath))
116 121 else:
... ... @@ -118,7 +123,7 @@ class LoadDicom:
118 123 reader.SetFileName(utils.encode(self.filepath, const.FS_ENCODE))
119 124 except TypeError:
120 125 reader.SetFileName(self.filepath)
121   - if (reader.Read()):
  126 + if reader.Read():
122 127 file = reader.GetFile()
123 128 # Retrieve data set
124 129 dataSet = file.GetDataSet()
... ... @@ -133,23 +138,23 @@ class LoadDicom:
133 138 tag = gdcm.Tag(0x0008, 0x0005)
134 139 ds = reader.GetFile().GetDataSet()
135 140 image_helper = gdcm.ImageHelper()
136   - data_dict['spacing'] = image_helper.GetSpacingValue(reader.GetFile())
  141 + data_dict["spacing"] = image_helper.GetSpacingValue(reader.GetFile())
137 142 if ds.FindDataElement(tag):
138   - encoding_value = str(ds.GetDataElement(tag).GetValue()).split('\\')[0]
139   -
  143 + encoding_value = str(ds.GetDataElement(tag).GetValue()).split("\\")[0]
  144 +
140 145 if encoding_value.startswith("Loaded"):
141 146 encoding = "ISO_IR 100"
142 147 else:
143 148 try:
144 149 encoding = const.DICOM_ENCODING_TO_PYTHON[encoding_value]
145 150 except KeyError:
146   - encoding = 'ISO_IR 100'
  151 + encoding = "ISO_IR 100"
147 152 else:
148 153 encoding = "ISO_IR 100"
149 154  
150 155 # Iterate through the Header
151 156 iterator = header.GetDES().begin()
152   - while (not iterator.equal(header.GetDES().end())):
  157 + while not iterator.equal(header.GetDES().end()):
153 158 dataElement = iterator.next()
154 159 if not dataElement.IsUndefinedLength():
155 160 tag = dataElement.GetTag()
... ... @@ -164,20 +169,20 @@ class LoadDicom:
164 169 if not group in data_dict.keys():
165 170 data_dict[group] = {}
166 171  
167   - if not(utils.VerifyInvalidPListCharacter(data[1])):
  172 + if not (utils.VerifyInvalidPListCharacter(data[1])):
168 173 data_dict[group][field] = utils.decode(data[1], encoding)
169 174 else:
170 175 data_dict[group][field] = "Invalid Character"
171 176  
172 177 # Iterate through the Data set
173 178 iterator = dataSet.GetDES().begin()
174   - while (not iterator.equal(dataSet.GetDES().end())):
  179 + while not iterator.equal(dataSet.GetDES().end()):
175 180 dataElement = iterator.next()
176 181 if not dataElement.IsUndefinedLength():
177 182 tag = dataElement.GetTag()
178 183 # if (tag.GetGroup() == 0x0009 and tag.GetElement() == 0x10e3) \
179   - # or (tag.GetGroup() == 0x0043 and tag.GetElement() == 0x1027):
180   - # continue
  184 + # or (tag.GetGroup() == 0x0043 and tag.GetElement() == 0x1027):
  185 + # continue
181 186 data = stf.ToStringPair(tag)
182 187 stag = tag.PrintAsPipeSeparatedString()
183 188  
... ... @@ -189,28 +194,28 @@ class LoadDicom:
189 194 if not group in data_dict.keys():
190 195 data_dict[group] = {}
191 196  
192   - if not(utils.VerifyInvalidPListCharacter(data[1])):
193   - data_dict[group][field] = utils.decode(data[1], encoding, 'replace')
  197 + if not (utils.VerifyInvalidPListCharacter(data[1])):
  198 + data_dict[group][field] = utils.decode(
  199 + data[1], encoding, "replace"
  200 + )
194 201 else:
195 202 data_dict[group][field] = "Invalid Character"
196 203  
197   -
198 204 # -------------- To Create DICOM Thumbnail -----------
199 205  
200   -
201 206 try:
202 207 data = data_dict[str(0x028)][str(0x1050)]
203   - level = [float(value) for value in data.split('\\')][0]
  208 + level = [float(value) for value in data.split("\\")][0]
204 209 data = data_dict[str(0x028)][str(0x1051)]
205   - window = [float(value) for value in data.split('\\')][0]
206   - except(KeyError, ValueError):
  210 + window = [float(value) for value in data.split("\\")][0]
  211 + except (KeyError, ValueError):
207 212 level = None
208 213 window = None
209 214  
210 215 img = reader.GetImage()
211 216 thumbnail_path = imagedata_utils.create_dicom_thumbnails(img, window, level)
212 217  
213   - #------ Verify the orientation --------------------------------
  218 + # ------ Verify the orientation --------------------------------
214 219  
215 220 direc_cosines = img.GetDirectionCosines()
216 221 orientation = gdcm.Orientation()
... ... @@ -220,41 +225,43 @@ class LoadDicom:
220 225 _type = orientation.GetType(direc_cosines)
221 226 label = orientation.GetLabel(_type)
222 227  
223   -
224 228 # ---------- Refactory --------------------------------------
225   - data_dict['invesalius'] = {'orientation_label' : label}
  229 + data_dict["invesalius"] = {"orientation_label": label}
226 230  
227 231 # -------------------------------------------------------------
228 232 dict_file[self.filepath] = data_dict
229   -
230   - #---------- Verify is DICOMDir -------------------------------
  233 +
  234 + # ---------- Verify is DICOMDir -------------------------------
231 235 is_dicom_dir = 1
232   - try:
233   - if (data_dict[str(0x002)][str(0x002)] != "1.2.840.10008.1.3.10"): #DICOMDIR
234   - is_dicom_dir = 0
235   - except(KeyError):
  236 + try:
  237 + if (
  238 + data_dict[str(0x002)][str(0x002)] != "1.2.840.10008.1.3.10"
  239 + ): # DICOMDIR
236 240 is_dicom_dir = 0
237   -
238   - if not(is_dicom_dir):
  241 + except (KeyError):
  242 + is_dicom_dir = 0
  243 +
  244 + if not (is_dicom_dir):
239 245 parser = dicom.Parser()
240   - parser.SetDataImage(dict_file[self.filepath], self.filepath, thumbnail_path)
241   -
  246 + parser.SetDataImage(
  247 + dict_file[self.filepath], self.filepath, thumbnail_path
  248 + )
  249 +
242 250 dcm = dicom.Dicom()
243   - #self.l.acquire()
  251 + # self.l.acquire()
244 252 dcm.SetParser(parser)
245 253 grouper.AddFile(dcm)
246 254  
247   - #self.l.release()
248   -
  255 + # self.l.release()
249 256  
250   - #========== used in test =======================================
251   - #print dict_file
252   - #main_dict = dict(
  257 + # ========== used in test =======================================
  258 + # print dict_file
  259 + # main_dict = dict(
253 260 # data = dict_file,
254 261 # labels = tag_labels)
255   - #print main_dict
256   - #print "\n"
257   - #plistlib.writePlist(main_dict, ".//teste.plist")
  262 + # print main_dict
  263 + # print "\n"
  264 + # plistlib.writePlist(main_dict, ".//teste.plist")
258 265  
259 266  
260 267 def yGetDicomGroups(directory, recursive=True, gui=True):
... ... @@ -271,11 +278,11 @@ def yGetDicomGroups(directory, recursive=True, gui=True):
271 278 nfiles = len(filenames)
272 279  
273 280 counter = 0
274   - grouper = dicom_grouper.DicomPatientGrouper()
275   - #q = Queue.Queue()
276   - #l = threading.Lock()
277   - #threads = []
278   - #for i in xrange(cpu_count()):
  281 + grouper = dicom_grouper.DicomPatientGrouper()
  282 + # q = Queue.Queue()
  283 + # l = threading.Lock()
  284 + # threads = []
  285 + # for i in xrange(cpu_count()):
279 286 # t = LoadDicom(grouper, q, l)
280 287 # t.start()
281 288 # threads.append(t)
... ... @@ -286,7 +293,7 @@ def yGetDicomGroups(directory, recursive=True, gui=True):
286 293 filepath = os.path.join(dirpath, name)
287 294 counter += 1
288 295 if gui:
289   - yield (counter,nfiles)
  296 + yield (counter, nfiles)
290 297 LoadDicom(grouper, filepath)
291 298 else:
292 299 dirpath, dirnames, filenames = os.walk(directory)
... ... @@ -294,17 +301,17 @@ def yGetDicomGroups(directory, recursive=True, gui=True):
294 301 filepath = str(os.path.join(dirpath, name))
295 302 counter += 1
296 303 if gui:
297   - yield (counter,nfiles)
298   - #q.put(filepath)
  304 + yield (counter, nfiles)
  305 + # q.put(filepath)
299 306  
300   - #for t in threads:
  307 + # for t in threads:
301 308 # q.put(0)
302 309  
303   - #for t in threads:
  310 + # for t in threads:
304 311 # t.join()
305 312  
306   - #TODO: Is this commented update necessary?
307   - #grouper.Update()
  313 + # TODO: Is this commented update necessary?
  314 + # grouper.Update()
308 315 yield grouper.GetPatientsGroups()
309 316  
310 317  
... ... @@ -321,14 +328,14 @@ class ProgressDicomReader:
321 328 self.stoped = True
322 329  
323 330 def SetWindowEvent(self, frame):
324   - self.frame = frame
  331 + self.frame = frame
325 332  
326   - def SetDirectoryPath(self, path,recursive=True):
  333 + def SetDirectoryPath(self, path, recursive=True):
327 334 self.running = True
328 335 self.stoped = False
329   - self.GetDicomGroups(path,recursive)
  336 + self.GetDicomGroups(path, recursive)
330 337  
331   - def UpdateLoadFileProgress(self,cont_progress):
  338 + def UpdateLoadFileProgress(self, cont_progress):
332 339 Publisher.sendMessage("Update dicom load", data=cont_progress)
333 340  
334 341 def EndLoadFile(self, patient_list):
... ... @@ -337,7 +344,9 @@ class ProgressDicomReader:
337 344 def GetDicomGroups(self, path, recursive):
338 345  
339 346 if not const.VTK_WARNING:
340   - log_path = utils.encode(str(inv_paths.USER_LOG_DIR.joinpath('vtkoutput.txt')), const.FS_ENCODE)
  347 + log_path = utils.encode(
  348 + str(inv_paths.USER_LOG_DIR.joinpath("vtkoutput.txt")), const.FS_ENCODE
  349 + )
341 350 fow = vtk.vtkFileOutputWindow()
342 351 fow.SetFileName(log_path)
343 352 ow = vtk.vtkOutputWindow()
... ... @@ -354,10 +363,8 @@ class ProgressDicomReader:
354 363 self.EndLoadFile(value_progress)
355 364 self.UpdateLoadFileProgress(None)
356 365  
357   - #Is necessary in the case user cancel
358   - #the load, ensure that dicomdialog is closed
359   - if(self.stoped):
  366 + # Is necessary in the case user cancel
  367 + # the load, ensure that dicomdialog is closed
  368 + if self.stoped:
360 369 self.UpdateLoadFileProgress(None)
361   - self.stoped = False
362   -
363   -
  370 + self.stoped = False
... ...