ADD: Part of the implementation new DICOM Class

Paulo Henrique Junqueira Amorim
1 parent fb59d2bd
Showing 2 changed files with 58 additions and 62 deletions Show diff stats
invesalius/reader/dicom_grouper.py
invesalius/reader/dicom_reader.py
@@ -51,7 +51,7 @@
 # <dicom.image.number> and <dicom.acquisition.series_number>
 # were swapped
-ORIENT_MAP = {"SAGITTAL":0, "AXIAL":1, "CORONAL":2}
+ORIENT_MAP = {"SAGITTAL":0, "CORONAL":1, "AXIAL":2}
 class DicomGroup:
@@ -65,10 +65,12 @@ class DicomGroup:
         # IDEA (13/10): Represent internally as dictionary,
         # externally as list
         self.nslices = 0
-
+        self.spacing = 0
+        
     def AddSlice(self, dicom):
-        pos = dicom.image.position 
+        pos = tuple(dicom.image.position) 
         if pos not in self.slices_dict.keys():
+            
             self.slices_dict[pos] = dicom
             self.nslices += 1
             return True
@@ -84,12 +86,27 @@ class DicomGroup:
     def GetSortedList(self):
         # This will be used to fix problem 1, after merging
         # single DicomGroups of same study_id and orientation
-        list_ = self.slices_dict_values()
-        axis = ORIENT_MAP[self.key[3]]
+        list_ = self.slices_dict.values()
+        dicom = list_[0]
+        axis = ORIENT_MAP[dicom.image.orientation_label]
         list_ = sorted(list_, key = lambda dicom:dicom.image.position[axis])
         return list_
-
+    def GetSpacing(self):
+        list_ = self.GetSortedList()
+        if (len(list_) > 1):
+            dicom = list_[0]
+            axis = ORIENT_MAP[dicom.image.orientation_label]
+            #print dicom.image.orientation_label
+            p1 = dicom.image.position[axis]
+            
+            dicom = list_[1]
+            p2 = dicom.image.position[axis]
+            
+            self.spacing = abs(p1 - p2)
+        else:
+            self.spacing = 1
+            
 class PatientGroup:
     def __init__(self):
         # key:
@@ -109,7 +126,7 @@ class PatientGroup:
         # implemented, dinamically during new dicom's addition
         group_key = (dicom.patient.name,
                      dicom.acquisition.id_study,
-                     dicom.acquisition.series_number,
+                     dicom.acquisition.serie_number,
                      dicom.image.orientation_label,
                      index) # This will be used to deal with Problem 2
@@ -120,13 +137,15 @@ class PatientGroup:
             self.groups_dict[group_key] = group
         # Group exists... Lets try to add slice
         else:
-            group = self.groups_dicom[group_key]
+            group = self.groups_dict[group_key]
             slice_added =  group.AddSlice(dicom)
             if not slice_added:
                 # If we're here, then Problem 2 occured
                 # TODO: Optimize recursion 
                 self.AddFile(file_path, index+1)
-
+        
+            group.GetSpacing()
+            
     def Update(self):
         # Ideally, AddFile would be sufficient for splitting DICOM
         # files into groups (series). However, this does not work for
@@ -144,7 +163,7 @@ class PatientGroup:
         # Fix Problem 1
         if is_there_problem_1:
             self.groups_dict = self.FixProblem1(self.groups_dict)
-
+            
     def GetGroups(self):
         return self.groups_dict.values()
@@ -231,18 +250,18 @@ class DicomPatientGrouper:
     # ... (repeat to all files on folder)
     # grouper.Update()
     # groups = GetPatientGroups()
-
+    
     def __init__(self):
         self.patients_dict = {}
-
+    
     def AddFile(self, dicom):
         patient_key = (dicom.patient.name,
                        dicom.patient.id)
-
+    
         # Does this patient exist?
         if patient_key not in self.patients_dict.keys():
             patient = PatientGroup()
-            patient.AddSlice(dicom)
+            patient.AddFile(dicom)
             self.patients_dict[patient_key] = patient
         # Patient exists... Lets add group to it
         else:
@@ -252,7 +271,7 @@ class DicomPatientGrouper:
     def Update(self):
         for patient in self.patients_dict.values():
             patient.Update()
-
+    
     def GetPatientsGroups(self):
         """
         How to use:
@@ -31,41 +31,22 @@ from data.imagedata_utils import ResampleImage2D
 def LoadImages(dir_):
     #  TODO!!! SUPER GAMBIARRA!!! DO THIS BETTER
-    dcm_files = GetDicomFiles(dir_)
-
-    dcm_series = dicom_grouper.DicomGroups()
-    dcm_series.SetFileList(dcm_files)
-    dcm_series.Update()
-
-    groups = dcm_series.GetOutput()
-
-    tmp_list = []
-    list_files = []
-
-    for x in xrange(len(groups.keys())):
-        key = groups.keys()[x]
-
-        for y in xrange(len(groups[key])):
-            dicom = groups[key][y]
-            file = dicom.image.file
-            tmp_list.append(file)
-
-        list_files.append([len(tmp_list), key])
-        tmp_list = []
-
-    if list_files:
-        key =  max(list_files)[1]
-    else:
-        return None
-
+    patient_group = GetDicomFiles(dir_)
+  
+    for patient in patient_group:
+        group_list = patient.GetGroups()
+        for group in group_list:
+            d = group.GetList()
+            spacing = group.spacing
+            
+    #dcm_series = dicom_grouper.DicomGroup()
+    #dcm_series.SetFileList(dcm_files)
+    #dcm_series.Update()
+   
     file_list = []
-    for x in xrange(len(groups[key])):
-        dicom = groups[key][x]
+    for dicom in d:
         file_list.append(dicom.image.file)
-    files = file_list
-    spacing = dicom.image.spacing
-    
     #Coronal Crash. necessary verify
     if (dicom.image.orientation_label <> "CORONAL"):
         #Organize reversed image
@@ -92,7 +73,7 @@ def LoadImages(dir_):
         image_data = vtk.vtkImageData()
         image_data.DeepCopy(read.GetOutput())
-        spacing = dicom.image.spacing
+        
         image_data.SetSpacing(spacing)
     else:
         for x in xrange(len(files)):
@@ -112,8 +93,7 @@ def LoadImages(dir_):
         image_data = vtk.vtkImageData()
         image_data.DeepCopy(img_app.GetOutput())
         image_data.SetSpacing(image_data.GetSpacing()[0],\
-                         image_data.GetSpacing()[1],\
-                         dicom.image.spacing[2])
+                         image_data.GetSpacing()[1], spacing)
     image_data.Update()
@@ -171,19 +151,16 @@ def GetDicomFiles(path):
     # FIXME: Currently recursion is not working
     # Recursivelly, find all files inside this folder
-    file_list = []
+    grouper = dicom_grouper.DicomPatientGrouper()
     for p in list_paths:
         p_file_list = p[-1]
         file_path = p[0]
         for filename in p_file_list:
-            file_list.append(str(os.path.join(file_path,filename)))
-
-    # Check if given file is in DICOM format
-    dicom_files = []
-    for file in file_list:
-        read_dicom = dicom.Parser()
-        if (read_dicom.SetFileName(file)):
-            dicom_files.append(file)
-
-
-    return dicom_files
+            file = str(os.path.join(file_path,filename))
+            parser = dicom.Parser()
+            if (parser.SetFileName(file)):
+                dcm = dicom.Dicom()
+                dcm.SetParser(parser)
+                grouper.AddFile(dcm)
+                
+    return grouper.GetPatientsGroups()