Download as
Browse Code »

Commit 0a8d35b25865f6fde0c25f7d1f0c407baf292f62

Authored by tatiana
1 parent 3dfaec66
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

ENC: Changed import panel's implementation

Showing 4 changed files with 56 additions and 113 deletions   Show diff stats
invesalius/control.py
  Diff comments   View file @0a8d35b
... ... @@ -35,56 +35,10 @@ class Controller():
35 35 path = pubsub_evt.data
36 36  
37 37 # retrieve DICOM files splited into groups
38   - dicom_series = dcm.GetSeries(path)
39   -
40   - # create dictionary with DICOM files' groups with
41   - # information as it will be shown on import panel
42   - dict = {}
43   - series_preview = []
44   -
45   - for key in dicom_series:
46   - patient_name = key[0]
47   - dicom = dicom_series[key][0]
48   -
49   - # Compute how many images per series:
50   - n_images = str(len(dicom_series[key]))
51   - # Add date and time in a single field:
52   - date_time = "%s %s"%(dicom.acquisition.date,
53   - dicom.acquisition.time)
54   -
55   - # Data per series
56   - exam_data = [dicom.acquisition.series_description,
57   - dicom.patient.id,
58   - str(dicom.patient.age),
59   - dicom.patient.gender,
60   - dicom.acquisition.study_description, # per patient
61   - dicom.acquisition.modality,
62   - date_time,
63   - n_images,
64   - dicom.acquisition.institution,
65   - dicom.patient.birthdate,
66   - dicom.acquisition.accession_number,
67   - dicom.patient.physician,
68   - dicom.acquisition.protocol_name] # per series
69   -
70   - # Preview data
71   - series_preview.append((dicom.image.file, # Filename
72   - dicom.image.level, # Window level
73   - dicom.image.window, # Window width
74   - dicom.acquisition.series_description, # Title
75   - "%s Images" %(n_images), # Subtitle
76   - ))
77   -
78   - try:
79   - dict[patient_name].append(exam_data)
80   - except KeyError:
81   - dict[patient_name] = [exam_data]
82   - print dict
83   -
84   -
  38 + dicom_series = dcm.GetDicomGroups(path)
  39 + ps.Publisher().sendMessage("Load import panel", dicom_series)
85 40  
86   - ps.Publisher().sendMessage("Load import panel", dict)
87   - ps.Publisher().sendMessage("Load dicom preview", series_preview)
  41 + #ps.Publisher().sendMessage("Load dicom preview", series_preview)
88 42  
89 43  
90 44 def ImportDirectory(self, pubsub_evt=None, dir_=None):
... ...
invesalius/gui/import_panel.py
  Diff comments   View file @0a8d35b
... ... @@ -40,8 +40,8 @@ class InnerPanel(wx.Panel):
40 40 ps.Publisher().subscribe(self.ShowDicomPreview, "Load import panel")
41 41  
42 42 def ShowDicomPreview(self, pubsub_evt):
43   - dict = pubsub_evt.data
44   - self.text_panel.Populate(dict)
  43 + dicom_groups = pubsub_evt.data
  44 + self.text_panel.Populate(dicom_groups)
45 45  
46 46  
47 47 class TextPanel(wx.Panel):
... ... @@ -92,64 +92,47 @@ class TextPanel(wx.Panel):
92 92 self.root = tree.AddRoot("InVesalius Database")
93 93 self.tree = tree
94 94  
95   - def Populate(self, dict):
  95 + def Populate(self, patient_list):
96 96 tree = self.tree
97 97  
98   - i = 0
  98 + for patient in patient_list:
  99 + ngroups = patient.ngroups
  100 + dicom = patient.GetDicomSample()
  101 + title = dicom.patient.name + " (%d series)"%(ngroups)
  102 + date_time = "%s %s"%(dicom.acquisition.date,
  103 + dicom.acquisition.time)
99 104  
100   - # For each patient on dictionary
101   - for patient_name in dict:
102   - # In spite of the patient name, we'll show number of
103   - # series also
104   - title = patient_name + " (%d series)"%(len(dict[patient_name]))
105 105 parent = tree.AppendItem(self.root, title)
106   - patient_data = dict[patient_name]
107   -
108   - # Row background colour
109   - if i%2:
110   - tree.SetItemBackgroundColour(parent, (242,246,254))
111   -
112   - # Insert patient data into columns based on first series
113   - for item in xrange(1, len(patient_data[0])-1):
114   - value = patient_data[0][item]
115   - # Sum slices of all patient's series
116   - if (item == 7):
117   - value = 0
118   - for series in xrange(len(patient_data)):
119   - value += int(patient_data[series][7])
120   - tree.SetItemText(parent, str(value), item) # ID
121   -
122   - # For each series on patient
123   - j = 0
124   - for series in xrange(len(patient_data)):
125   - series_title = patient_data[series][0]
126   -
127   - child = self.tree.AppendItem(parent, series_title)
128   - if not j%2:
129   - tree.SetItemBackgroundColour(child, (242,246,254))
130   -
131   - # TODO: change description "protocol_name"
132   - description = patient_data[series][-1]
133   - modality = patient_data[series][5]
134   - # TODO: add to date the time
135   - date = patient_data[series][6]
136   - nimages = patient_data[series][7]
137   -
138   - tree.SetItemText(child, series_title, 0)
139   - tree.SetItemText(child, description, 4)
140   - tree.SetItemText(child, modality, 5)
141   - tree.SetItemText(child, date, 6)
142   - tree.SetItemText(child, nimages, 7)
143   -
144   - j += 1
145   - i += 1
146   -
  106 + tree.SetItemText(parent, str(dicom.patient.id), 1)
  107 + tree.SetItemText(parent, str(dicom.patient.age), 2)
  108 + tree.SetItemText(parent, str(dicom.patient.gender), 3)
  109 + tree.SetItemText(parent, str(dicom.acquisition.study_description), 4)
  110 + tree.SetItemText(parent, str(dicom.acquisition.modality), 5)
  111 + tree.SetItemText(parent, str(date_time), 6)
  112 + tree.SetItemText(parent, str(patient.nslices), 7)
  113 + tree.SetItemText(parent, str(dicom.acquisition.institution), 8)
  114 + tree.SetItemText(parent, str(dicom.patient.birthdate), 9)
  115 + tree.SetItemText(parent, str(dicom.acquisition.accession_number), 10)
  116 + tree.SetItemText(parent, str(dicom.patient.physician), 11)
  117 +
  118 + group_list = patient.GetGroups()
  119 + for group in group_list:
  120 + dicom = group.GetDicomSample()
  121 + group_title = dicom.acquisition.series_description
  122 +
  123 + child = self.tree.AppendItem(parent, group_title)
  124 +
  125 + tree.SetItemText(child, str(group_title), 0)
  126 + tree.SetItemText(child, str(dicom.acquisition.protocol_name), 4)
  127 + tree.SetItemText(child, str(dicom.acquisition.modality), 5)
  128 + tree.SetItemText(child, str(date_time), 6)
  129 + tree.SetItemText(child, str(group.nslices), 7)
  130 +
147 131 tree.Expand(self.root)
148 132  
149 133 tree.GetMainWindow().Bind(wx.EVT_RIGHT_UP, self.OnRightUp)
150 134 tree.Bind(wx.EVT_TREE_ITEM_ACTIVATED, self.OnActivate)
151 135  
152   -
153 136 def OnActivate(self, evt):
154 137 print 'OnActivate: %s' % self.tree.GetItemText(evt.GetItem())
155 138  
... ...
invesalius/reader/dicom_grouper.py
  Diff comments   View file @0a8d35b
... ... @@ -66,11 +66,13 @@ class DicomGroup:
66 66 # externally as list
67 67 self.nslices = 0
68 68 self.zspacing = 1
  69 + self.dicom = None
69 70  
70 71 def AddSlice(self, dicom):
  72 + if not self.dicom:
  73 + self.dicom = dicom
71 74 pos = tuple(dicom.image.position)
72 75 if pos not in self.slices_dict.keys():
73   -
74 76 self.slices_dict[pos] = dicom
75 77 self.nslices += 1
76 78 return True
... ... @@ -106,6 +108,9 @@ class DicomGroup:
106 108 self.zspacing = abs(p1 - p2)
107 109 else:
108 110 self.zspacing = 1
  111 +
  112 + def GetDicomSample(self):
  113 + return self.dicom
109 114  
110 115 class PatientGroup:
111 116 def __init__(self):
... ... @@ -114,6 +119,8 @@ class PatientGroup:
114 119 self.key = ()
115 120 self.groups_dict = {} # group_key: DicomGroup
116 121 self.nslices = 0
  122 + self.ngroups = 0
  123 + self.dicom = None
117 124  
118 125 def AddFile(self, dicom, index=0):
119 126 # Given general DICOM information, we group slices according
... ... @@ -129,10 +136,14 @@ class PatientGroup:
129 136 dicom.acquisition.serie_number,
130 137 dicom.image.orientation_label,
131 138 index) # This will be used to deal with Problem 2
  139 + if not self.dicom:
  140 + self.dicom = dicom
  141 +
132 142 self.nslices += 1
133 143 # Does this group exist? Best case ;)
134 144 if group_key not in self.groups_dict.keys():
135 145 group = DicomGroup()
  146 + self.ngroups += 1
136 147 group.AddSlice(dicom)
137 148 self.groups_dict[group_key] = group
138 149 # Group exists... Lets try to add slice
... ... @@ -168,6 +179,9 @@ class PatientGroup:
168 179 def GetGroups(self):
169 180 return self.groups_dict.values()
170 181  
  182 + def GetDicomSample(self):
  183 + return self.dicom
  184 +
171 185 def FixProblem1(self, dict):
172 186 """
173 187 Merge multiple DICOM groups in case Problem 1 (description
... ... @@ -268,6 +282,7 @@ class DicomPatientGrouper:
268 282 # Does this patient exist?
269 283 if patient_key not in self.patients_dict.keys():
270 284 patient = PatientGroup()
  285 + patient.key = patient_key
271 286 patient.AddFile(dicom)
272 287 self.patients_dict[patient_key] = patient
273 288 # Patient exists... Lets add group to it
... ... @@ -290,5 +305,7 @@ class DicomPatientGrouper:
290 305 # :) you've got a list of dicom.Dicom
291 306 # of the same series
292 307 """
293   - return self.patients_dict.values()
  308 + plist = self.patients_dict.values()
  309 + plist = sorted(plist, key = lambda patient:patient.key[0])
  310 + return plist
294 311  
... ...
invesalius/reader/dicom_reader.py
  Diff comments   View file @0a8d35b
... ... @@ -118,17 +118,6 @@ def CreateImageData(filelist, zspacing):
118 118 imagedata.Update()
119 119 return imagedata
120 120  
121   -def GetSeries(path):
122   - """
123   - Return DICOM group of files inside given directory.
124   - """
125   - dcm_files = GetDicomFiles(path)
126   -
127   - dcm_series = dicom_grouper.DicomGroups()
128   - dcm_series.SetFileList(dcm_files)
129   - dcm_series.Update()
130   -
131   - return dcm_series.GetOutput()
132 121  
133 122 def GetDicomGroups(directory, recursive=True):
134 123 """
... ...