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Commit 75348ea4ec0a625f865d08024aa18e655c755741

Authored by Paulo Henrique Junqueira Amorim
1 parent fb59d2bd
Exists in master and in 68 other branches 3d_inter_style, MIPs, beta3, beta4, brush_pix, canvas_reeng, canvas_text, casmoothing_cython, clean, command-line, cython_threshold, debian_cython, editor_improvements, encoding, ff_mask, ff_mask_improv, ffill_gui, ffill_segmentation, fill_holes_auto, fixes_pre_beta5, floodfill, get_pixel, import_mesh, interactor_style, inv3.0.1, invesalius-libift, mactoolbar, mactoolbar_bkp, manual_v3.1, mask_boolean_op, mask_boolean_op_bkp, mask_copy, mask_greatest_component, measure, measure_canvas, measure_improvements, measure_placement_test, measure_spacing, orientation, phoenix, region_growing_confidence, remote, remove_local_wxpython, rmatsuda-fix_ref_MTC, rmatsuda-fix_remove_marker_bug, rmatsuda-trigger_bug_fix, rotvol, segmentation_menu, select_part, smoothing_bin, smoothing_bin_pll, surface_area, threshold_history, user_guide_en, usp-navegador, vti, vtk6, watershed, watershed_improvements, watershed_improvements_bkp, watershed_merge, workdir, wwwlgui, wx2.9_mac, wxgtk3, wxgtk3_b5, wxgtk3_bkp, xmartlabs-command-line

ADD: Part of the implementation new DICOM Class

Showing 2 changed files with 58 additions and 62 deletions   Show diff stats
invesalius/reader/dicom_grouper.py
  Diff comments   View file @75348ea
... ... @@ -51,7 +51,7 @@
51 51 # <dicom.image.number> and <dicom.acquisition.series_number>
52 52 # were swapped
53 53  
54   -ORIENT_MAP = {"SAGITTAL":0, "AXIAL":1, "CORONAL":2}
  54 +ORIENT_MAP = {"SAGITTAL":0, "CORONAL":1, "AXIAL":2}
55 55  
56 56  
57 57 class DicomGroup:
... ... @@ -65,10 +65,12 @@ class DicomGroup:
65 65 # IDEA (13/10): Represent internally as dictionary,
66 66 # externally as list
67 67 self.nslices = 0
68   -
  68 + self.spacing = 0
  69 +
69 70 def AddSlice(self, dicom):
70   - pos = dicom.image.position
  71 + pos = tuple(dicom.image.position)
71 72 if pos not in self.slices_dict.keys():
  73 +
72 74 self.slices_dict[pos] = dicom
73 75 self.nslices += 1
74 76 return True
... ... @@ -84,12 +86,27 @@ class DicomGroup:
84 86 def GetSortedList(self):
85 87 # This will be used to fix problem 1, after merging
86 88 # single DicomGroups of same study_id and orientation
87   - list_ = self.slices_dict_values()
88   - axis = ORIENT_MAP[self.key[3]]
  89 + list_ = self.slices_dict.values()
  90 + dicom = list_[0]
  91 + axis = ORIENT_MAP[dicom.image.orientation_label]
89 92 list_ = sorted(list_, key = lambda dicom:dicom.image.position[axis])
90 93 return list_
91 94  
92   -
  95 + def GetSpacing(self):
  96 + list_ = self.GetSortedList()
  97 + if (len(list_) > 1):
  98 + dicom = list_[0]
  99 + axis = ORIENT_MAP[dicom.image.orientation_label]
  100 + #print dicom.image.orientation_label
  101 + p1 = dicom.image.position[axis]
  102 +
  103 + dicom = list_[1]
  104 + p2 = dicom.image.position[axis]
  105 +
  106 + self.spacing = abs(p1 - p2)
  107 + else:
  108 + self.spacing = 1
  109 +
93 110 class PatientGroup:
94 111 def __init__(self):
95 112 # key:
... ... @@ -109,7 +126,7 @@ class PatientGroup:
109 126 # implemented, dinamically during new dicom's addition
110 127 group_key = (dicom.patient.name,
111 128 dicom.acquisition.id_study,
112   - dicom.acquisition.series_number,
  129 + dicom.acquisition.serie_number,
113 130 dicom.image.orientation_label,
114 131 index) # This will be used to deal with Problem 2
115 132  
... ... @@ -120,13 +137,15 @@ class PatientGroup:
120 137 self.groups_dict[group_key] = group
121 138 # Group exists... Lets try to add slice
122 139 else:
123   - group = self.groups_dicom[group_key]
  140 + group = self.groups_dict[group_key]
124 141 slice_added = group.AddSlice(dicom)
125 142 if not slice_added:
126 143 # If we're here, then Problem 2 occured
127 144 # TODO: Optimize recursion
128 145 self.AddFile(file_path, index+1)
129   -
  146 +
  147 + group.GetSpacing()
  148 +
130 149 def Update(self):
131 150 # Ideally, AddFile would be sufficient for splitting DICOM
132 151 # files into groups (series). However, this does not work for
... ... @@ -144,7 +163,7 @@ class PatientGroup:
144 163 # Fix Problem 1
145 164 if is_there_problem_1:
146 165 self.groups_dict = self.FixProblem1(self.groups_dict)
147   -
  166 +
148 167 def GetGroups(self):
149 168 return self.groups_dict.values()
150 169  
... ... @@ -231,18 +250,18 @@ class DicomPatientGrouper:
231 250 # ... (repeat to all files on folder)
232 251 # grouper.Update()
233 252 # groups = GetPatientGroups()
234   -
  253 +
235 254 def __init__(self):
236 255 self.patients_dict = {}
237   -
  256 +
238 257 def AddFile(self, dicom):
239 258 patient_key = (dicom.patient.name,
240 259 dicom.patient.id)
241   -
  260 +
242 261 # Does this patient exist?
243 262 if patient_key not in self.patients_dict.keys():
244 263 patient = PatientGroup()
245   - patient.AddSlice(dicom)
  264 + patient.AddFile(dicom)
246 265 self.patients_dict[patient_key] = patient
247 266 # Patient exists... Lets add group to it
248 267 else:
... ... @@ -252,7 +271,7 @@ class DicomPatientGrouper:
252 271 def Update(self):
253 272 for patient in self.patients_dict.values():
254 273 patient.Update()
255   -
  274 +
256 275 def GetPatientsGroups(self):
257 276 """
258 277 How to use:
... ...
invesalius/reader/dicom_reader.py
  Diff comments   View file @75348ea
... ... @@ -31,41 +31,22 @@ from data.imagedata_utils import ResampleImage2D
31 31 def LoadImages(dir_):
32 32 # TODO!!! SUPER GAMBIARRA!!! DO THIS BETTER
33 33  
34   - dcm_files = GetDicomFiles(dir_)
35   -
36   - dcm_series = dicom_grouper.DicomGroups()
37   - dcm_series.SetFileList(dcm_files)
38   - dcm_series.Update()
39   -
40   - groups = dcm_series.GetOutput()
41   -
42   - tmp_list = []
43   - list_files = []
44   -
45   - for x in xrange(len(groups.keys())):
46   - key = groups.keys()[x]
47   -
48   - for y in xrange(len(groups[key])):
49   - dicom = groups[key][y]
50   - file = dicom.image.file
51   - tmp_list.append(file)
52   -
53   - list_files.append([len(tmp_list), key])
54   - tmp_list = []
55   -
56   - if list_files:
57   - key = max(list_files)[1]
58   - else:
59   - return None
60   -
  34 + patient_group = GetDicomFiles(dir_)
  35 +
  36 + for patient in patient_group:
  37 + group_list = patient.GetGroups()
  38 + for group in group_list:
  39 + d = group.GetList()
  40 + spacing = group.spacing
  41 +
  42 + #dcm_series = dicom_grouper.DicomGroup()
  43 + #dcm_series.SetFileList(dcm_files)
  44 + #dcm_series.Update()
  45 +
61 46 file_list = []
62   - for x in xrange(len(groups[key])):
63   - dicom = groups[key][x]
  47 + for dicom in d:
64 48 file_list.append(dicom.image.file)
65 49  
66   - files = file_list
67   - spacing = dicom.image.spacing
68   -
69 50 #Coronal Crash. necessary verify
70 51 if (dicom.image.orientation_label <> "CORONAL"):
71 52 #Organize reversed image
... ... @@ -92,7 +73,7 @@ def LoadImages(dir_):
92 73  
93 74 image_data = vtk.vtkImageData()
94 75 image_data.DeepCopy(read.GetOutput())
95   - spacing = dicom.image.spacing
  76 +
96 77 image_data.SetSpacing(spacing)
97 78 else:
98 79 for x in xrange(len(files)):
... ... @@ -112,8 +93,7 @@ def LoadImages(dir_):
112 93 image_data = vtk.vtkImageData()
113 94 image_data.DeepCopy(img_app.GetOutput())
114 95 image_data.SetSpacing(image_data.GetSpacing()[0],\
115   - image_data.GetSpacing()[1],\
116   - dicom.image.spacing[2])
  96 + image_data.GetSpacing()[1], spacing)
117 97  
118 98 image_data.Update()
119 99  
... ... @@ -171,19 +151,16 @@ def GetDicomFiles(path):
171 151  
172 152 # FIXME: Currently recursion is not working
173 153 # Recursivelly, find all files inside this folder
174   - file_list = []
  154 + grouper = dicom_grouper.DicomPatientGrouper()
175 155 for p in list_paths:
176 156 p_file_list = p[-1]
177 157 file_path = p[0]
178 158 for filename in p_file_list:
179   - file_list.append(str(os.path.join(file_path,filename)))
180   -
181   - # Check if given file is in DICOM format
182   - dicom_files = []
183   - for file in file_list:
184   - read_dicom = dicom.Parser()
185   - if (read_dicom.SetFileName(file)):
186   - dicom_files.append(file)
187   -
188   -
189   - return dicom_files
  159 + file = str(os.path.join(file_path,filename))
  160 + parser = dicom.Parser()
  161 + if (parser.SetFileName(file)):
  162 + dcm = dicom.Dicom()
  163 + dcm.SetParser(parser)
  164 + grouper.AddFile(dcm)
  165 +
  166 + return grouper.GetPatientsGroups()
... ...