FIX: Bug in the FixProblem1 error getting z spacing

Paulo Henrique Junqueira Amorim
1 parent 7ed6d001
Showing 1 changed file with 17 additions and 10 deletions Show diff stats
invesalius/reader/dicom_grouper.py
@@ -114,7 +114,7 @@ class PatientGroup:
         # (dicom.patient.name, dicom.patient.id)
         self.key = ()
         self.groups_dict = {} # group_key: DicomGroup
-        self.slices = 0
+        self.nslices = 0
  
     def AddFile(self, dicom, index=0):
         # Given general DICOM information, we group slices according
@@ -130,7 +130,7 @@ class PatientGroup:
                      dicom.acquisition.serie_number,
                      dicom.image.orientation_label,
                      index) # This will be used to deal with Problem 2
-        
+        self.nslices += 1
         # Does this group exist? Best case ;)
         if group_key not in self.groups_dict.keys():
             group = DicomGroup()
@@ -144,9 +144,10 @@ class PatientGroup:
                 # If we're here, then Problem 2 occured
                 # TODO: Optimize recursion 
                 self.AddFile(dicom, index+1)
-        
-            group.GetSpacing()
-            
+                
+                #Getting the spacing in the Z axis
+                group.GetSpacing()
+                    
     def Update(self):
         # Ideally, AddFile would be sufficient for splitting DICOM
         # files into groups (series). However, this does not work for
@@ -157,14 +158,14 @@ class PatientGroup:
  
         # Check if Problem 1 occurs (n groups with 1 slice each)
         is_there_problem_1 = False
-        if (self.ndicom == len(self.groups_dicom)) and\
-                (self.ndicom > 1):
+        if (self.nslices == len(self.groups_dict)) and\
+                (self.nslices > 1):
             is_there_problem_1 = True
  
         # Fix Problem 1
         if is_there_problem_1:
             self.groups_dict = self.FixProblem1(self.groups_dict)
-            
+        
     def GetGroups(self):
         return self.groups_dict.values()
  
@@ -192,8 +193,9 @@ class PatientGroup:
         # 1st STEP: RE-GROUP
         for group_key in dict:
             # values used as key of the new dictionary
-            orientation = dict[group_key].image.orientation_label
-            study_id = dict[group_key].acquisition.id_study
+            dicom = dict[group_key].GetList()[0]
+            orientation = dicom.image.orientation_label
+            study_id = dicom.acquisition.id_study
             # if axial, coronal or sagittal 
             if orientation in ORIENT_MAP:
                 group_key_s = (orientation, study_id)
@@ -234,11 +236,16 @@ class PatientGroup:
                         group = DicomGroup()
                         group.AddSlice(current)
                         dict_final[group_counter] = group
+                        #Getting the spacing in the Z axis
+                        group.GetSpacing()
                 else:
                     group_counter +=1
                     group = DicomGroup()
                     group.AddSlice(current)
                     dict_final[group_counter] = group
+                    #Getting the spacing in the Z axis
+                    group.GetSpacing()
+                
  
         return dict_final
...	...	@@ -114,7 +114,7 @@ class PatientGroup:
114	114	# (dicom.patient.name, dicom.patient.id)
115	115	self.key = ()
116	116	self.groups_dict = {} # group_key: DicomGroup
117		- self.slices = 0
	117	+ self.nslices = 0
118	118
119	119	def AddFile(self, dicom, index=0):
120	120	# Given general DICOM information, we group slices according
...	...	@@ -130,7 +130,7 @@ class PatientGroup:
130	130	dicom.acquisition.serie_number,
131	131	dicom.image.orientation_label,
132	132	index) # This will be used to deal with Problem 2
133		-
	133	+ self.nslices += 1
134	134	# Does this group exist? Best case ;)
135	135	if group_key not in self.groups_dict.keys():
136	136	group = DicomGroup()
...	...	@@ -144,9 +144,10 @@ class PatientGroup:
144	144	# If we're here, then Problem 2 occured
145	145	# TODO: Optimize recursion
146	146	self.AddFile(dicom, index+1)
147		-
148		- group.GetSpacing()
149		-
	147	+
	148	+ #Getting the spacing in the Z axis
	149	+ group.GetSpacing()
	150	+
150	151	def Update(self):
151	152	# Ideally, AddFile would be sufficient for splitting DICOM
152	153	# files into groups (series). However, this does not work for
...	...	@@ -157,14 +158,14 @@ class PatientGroup:
157	158
158	159	# Check if Problem 1 occurs (n groups with 1 slice each)
159	160	is_there_problem_1 = False
160		- if (self.ndicom == len(self.groups_dicom)) and\
161		- (self.ndicom > 1):
	161	+ if (self.nslices == len(self.groups_dict)) and\
	162	+ (self.nslices > 1):
162	163	is_there_problem_1 = True
163	164
164	165	# Fix Problem 1
165	166	if is_there_problem_1:
166	167	self.groups_dict = self.FixProblem1(self.groups_dict)
167		-
	168	+
168	169	def GetGroups(self):
169	170	return self.groups_dict.values()
170	171
...	...	@@ -192,8 +193,9 @@ class PatientGroup:
192	193	# 1st STEP: RE-GROUP
193	194	for group_key in dict:
194	195	# values used as key of the new dictionary
195		- orientation = dict[group_key].image.orientation_label
196		- study_id = dict[group_key].acquisition.id_study
	196	+ dicom = dict[group_key].GetList()[0]
	197	+ orientation = dicom.image.orientation_label
	198	+ study_id = dicom.acquisition.id_study
197	199	# if axial, coronal or sagittal
198	200	if orientation in ORIENT_MAP:
199	201	group_key_s = (orientation, study_id)
...	...	@@ -234,11 +236,16 @@ class PatientGroup:
234	236	group = DicomGroup()
235	237	group.AddSlice(current)
236	238	dict_final[group_counter] = group
	239	+ #Getting the spacing in the Z axis
	240	+ group.GetSpacing()
237	241	else:
238	242	group_counter +=1
239	243	group = DicomGroup()
240	244	group.AddSlice(current)
241	245	dict_final[group_counter] = group
	246	+ #Getting the spacing in the Z axis
	247	+ group.GetSpacing()
	248	+
242	249
243	250	return dict_final
244	251
...	...