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Commit 61d6ebfa72727b21617892f7b14ef792c3bcb050

Authored by Paulo Henrique Junqueira Amorim
1 parent d6839add
Exists in master and in 67 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, 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

ENH: Turned thread support in importation

Showing 2 changed files with 158 additions and 203 deletions   Show diff stats
invesalius/control.py
  Diff comments   View file @61d6ebf
@@ -120,12 +120,13 @@ class Controller(): @@ -120,12 +120,13 @@ class Controller():
120 answer = dialog.SaveChangesDialog2(filename) 120 answer = dialog.SaveChangesDialog2(filename)
121 if answer: 121 if answer:
122 self.ShowDialogSaveProject() 122 self.ShowDialogSaveProject()
123 -  
124 # Import project 123 # Import project
125 dirpath = dialog.ShowImportDirDialog() 124 dirpath = dialog.ShowImportDirDialog()
126 if dirpath and not os.listdir(dirpath): 125 if dirpath and not os.listdir(dirpath):
  126 + print "IFFFFFFFfff"
127 dialog.ImportEmptyDirectory(dirpath) 127 dialog.ImportEmptyDirectory(dirpath)
128 elif dirpath: 128 elif dirpath:
  129 + print "ELSE..........."
129 self.StartImportPanel(dirpath) 130 self.StartImportPanel(dirpath)
130 ps.Publisher().sendMessage("Load data to import panel", dirpath) 131 ps.Publisher().sendMessage("Load data to import panel", dirpath)
131 132
invesalius/reader/dicom_reader.py
  Diff comments   View file @61d6ebf
@@ -79,60 +79,132 @@ def SortFiles(filelist, dicom): @@ -79,60 +79,132 @@ def SortFiles(filelist, dicom):
79 79
80 return filelist 80 return filelist
81 81
82 -""" 82 +tag_labels = {}
  83 +main_dict = {}
  84 +dict_file = {}
  85 +
83 class LoadDicom(threading.Thread): 86 class LoadDicom(threading.Thread):
  87 +
84 def __init__(self, grouper, q, l): 88 def __init__(self, grouper, q, l):
85 threading.Thread.__init__(self) 89 threading.Thread.__init__(self)
86 self.grouper = grouper 90 self.grouper = grouper
87 self.q = q 91 self.q = q
88 self.l = l 92 self.l = l
  93 +
89 def run(self): 94 def run(self):
  95 +
90 grouper = self.grouper 96 grouper = self.grouper
91 q = self.q 97 q = self.q
  98 +
92 while 1: 99 while 1:
  100 +
93 filepath = q.get() 101 filepath = q.get()
94 if not filepath: 102 if not filepath:
95 break 103 break
96 - parser = dicom.Parser()  
97 - #if parser.SetFileName(filepath):  
98 - dcm = dicom.Dicom()  
99 - self.l.acquire()  
100 - dcm.SetParser(parser)  
101 - grouper.AddFile(dcm)  
102 - self.l.release()  
103 -"""  
104 -  
105 -"""  
106 -class LoadDicom():  
107 - def __init__(self, grouper, dicom_dict):  
108 - self.grouper = grouper  
109 - self.dicom_dict = dicom_dict 104 +
  105 + reader = gdcm.Reader()
  106 + reader.SetFileName(filepath)
  107 +
  108 + if (reader.Read()):
  109 +
  110 + file = reader.GetFile()
  111 +
  112 + # Retrieve data set
  113 + dataSet = file.GetDataSet()
  114 +
  115 + # Retrieve header
  116 + header = file.GetHeader()
  117 + stf = gdcm.StringFilter()
  118 +
  119 + field_dict = {}
  120 + data_dict = {}
  121 +
  122 +
  123 + tag = gdcm.Tag(0x0008, 0x0005)
  124 + ds = reader.GetFile().GetDataSet()
  125 + if ds.FindDataElement(tag):
  126 + encoding = str(ds.GetDataElement(tag).GetValue())
  127 + if not(encoding != None and encoding != "None" and encoding != "Loaded"):
  128 + encoding = "ISO_IR 100"
  129 + else:
  130 + encoding = "ISO_IR_100"
  131 + # Iterate through the Header
  132 + iterator = header.GetDES().begin()
  133 + while (not iterator.equal(header.GetDES().end())):
  134 + dataElement = iterator.next()
  135 + stf.SetFile(file)
  136 + tag = dataElement.GetTag()
  137 + data = stf.ToStringPair(tag)
  138 + stag = tag.PrintAsPipeSeparatedString()
  139 +
  140 + group = stag.split("|")[0][1:]
  141 + field = stag.split("|")[1][:-1]
  142 + tag_labels[stag] = data[0]
  143 +
  144 + if not group in data_dict.keys():
  145 + data_dict[group] = {}
  146 +
  147 + if not(utils.VerifyInvalidPListCharacter(data[1])):
  148 + data_dict[group][field] = data[1].decode(encoding)
  149 + else:
  150 + data_dict[group][field] = "Invalid Character"
110 151
111 - def Start(self):  
112 - images = self.dicom_dict['data']  
113 152
114 - grouper = self.grouper  
115 -  
116 - for x in images.keys():  
117 - data_image = images[x]  
118 - parser = dicom.Parser()  
119 - parser.SetDataImage(data_image)  
120 -  
121 - dcm = dicom.Dicom()  
122 - dcm.SetParser(parser)  
123 - grouper.AddFile(dcm)  
124 -  
125 -  
126 - #while 1:  
127 - #filepath = path  
128 - #if not filepath:  
129 - # break  
130 - #parser = dicom.Parser()  
131 - #if parser.SetFileName(filepath):  
132 - # dcm = dicom.Dicom()  
133 - # dcm.SetParser(parser)  
134 - # grouper.AddFile(dcm)  
135 -""" 153 + # Iterate through the Data set
  154 + iterator = dataSet.GetDES().begin()
  155 + while (not iterator.equal(dataSet.GetDES().end())):
  156 + dataElement = iterator.next()
  157 +
  158 + stf.SetFile(file)
  159 + tag = dataElement.GetTag()
  160 + data = stf.ToStringPair(tag)
  161 + stag = tag.PrintAsPipeSeparatedString()
  162 +
  163 + group = stag.split("|")[0][1:]
  164 + field = stag.split("|")[1][:-1]
  165 + tag_labels[stag] = data[0]
  166 +
  167 + if not group in data_dict.keys():
  168 + data_dict[group] = {}
  169 +
  170 + if not(utils.VerifyInvalidPListCharacter(data[1])):
  171 + data_dict[group][field] = data[1].decode(encoding)
  172 + else:
  173 + data_dict[group][field] = "Invalid Character"
  174 +
  175 +
  176 +
  177 + # ---------- Refactory --------------------------------------
  178 + data_dict['invesalius'] = {'orientation_label' : GetImageOrientationLabel(filepath)}
  179 +
  180 + # -------------------------------------------------------------
  181 + dict_file[filepath] = data_dict
  182 +
  183 + #---------- Verify is DICOMDir -------------------------------
  184 + is_dicom_dir = 1
  185 + try:
  186 + if (data_dict['0002']['0002'] != "1.2.840.10008.1.3.10"): #DICOMDIR
  187 + is_dicom_dir = 0
  188 + except(KeyError):
  189 + is_dicom_dir = 0
  190 +
  191 + if not(is_dicom_dir):
  192 + parser = dicom.Parser()
  193 + parser.SetDataImage(dict_file[filepath], filepath)
  194 +
  195 + dcm = dicom.Dicom()
  196 + self.l.acquire()
  197 + dcm.SetParser(parser)
  198 + grouper.AddFile(dcm)
  199 +
  200 + self.l.release()
  201 +
  202 + #========== used in test =======================================
  203 + #main_dict = dict(
  204 + # data = dict_file,
  205 + # labels = tag_labels)
  206 +
  207 + #plistlib.writePlist(main_dict, ".//teste.plist")"""
136 208
137 209
138 def GetImageOrientationLabel(filename): 210 def GetImageOrientationLabel(filename):
@@ -158,180 +230,60 @@ def GetImageOrientationLabel(filename): @@ -158,180 +230,60 @@ def GetImageOrientationLabel(filename):
158 else: 230 else:
159 return "" 231 return ""
160 232
161 -grouper = dicom_grouper.DicomPatientGrouper()  
162 233
163 -def GetDicomGroups(directory, recursive=True, gui=True): 234 +def yGetDicomGroups(directory, recursive=True, gui=True):
164 """ 235 """
165 Return all full paths to DICOM files inside given directory. 236 Return all full paths to DICOM files inside given directory.
166 """ 237 """
167 -  
168 nfiles = 0 238 nfiles = 0
169 # Find total number of files 239 # Find total number of files
170 if recursive: 240 if recursive:
171 -  
172 - folders = [f[0] for f in os.walk(directory)]  
173 -  
174 - tag_labels = {}  
175 - main_dict = {}  
176 - dict_file = {}  
177 -  
178 - for folder in folders:  
179 - files = glob.glob(os.path.join(folder, "*"))  
180 -  
181 - for filename in files:  
182 -  
183 - # Read file  
184 - reader = gdcm.Reader()  
185 - reader.SetFileName(filename)  
186 -  
187 - if (reader.Read()):  
188 -  
189 - file = reader.GetFile()  
190 -  
191 - # Retrieve data set  
192 - dataSet = file.GetDataSet()  
193 -  
194 - # Retrieve header  
195 - header = file.GetHeader()  
196 - stf = gdcm.StringFilter()  
197 -  
198 - field_dict = {}  
199 - data_dict = {}  
200 - 241 + for dirpath, dirnames, filenames in os.walk(directory):
  242 + nfiles += len(filenames)
  243 + else:
  244 + dirpath, dirnames, filenames = os.walk(directory)
  245 + nfiles = len(filenames)
  246 +
  247 + counter = 0
  248 + grouper = dicom_grouper.DicomPatientGrouper()
  249 + q = Queue.Queue()
  250 + l = threading.Lock()
  251 + threads = []
  252 + for i in xrange(cpu_count()):
  253 + t = LoadDicom(grouper, q, l)
  254 + t.start()
  255 + threads.append(t)
  256 + # Retrieve only DICOM files, splited into groups
  257 + if recursive:
  258 + for dirpath, dirnames, filenames in os.walk(directory):
  259 + for name in filenames:
  260 + filepath = os.path.join(dirpath, name)
  261 + counter += 1
  262 + if gui:
  263 + yield (counter,nfiles)
  264 + q.put(filepath)
  265 + else:
  266 + dirpath, dirnames, filenames = os.walk(directory)
  267 + for name in filenames:
  268 + filepath = str(os.path.join(dirpath, name))
  269 + counter += 1
  270 + if gui:
  271 + yield (counter,nfiles)
  272 + q.put(filepath)
201 273
202 - tag = gdcm.Tag(0x0008, 0x0005)  
203 - ds = reader.GetFile().GetDataSet()  
204 - if ds.FindDataElement(tag):  
205 - encoding = str(ds.GetDataElement(tag).GetValue())  
206 - if not(encoding != None and encoding != "None" and encoding != "Loaded"):  
207 - encoding = "ISO_IR 100"  
208 - else:  
209 - encoding = "ISO_IR_100"  
210 - # Iterate through the Header  
211 - iterator = header.GetDES().begin()  
212 - while (not iterator.equal(header.GetDES().end())):  
213 - dataElement = iterator.next()  
214 - stf.SetFile(file)  
215 - tag = dataElement.GetTag()  
216 - data = stf.ToStringPair(tag)  
217 - stag = tag.PrintAsPipeSeparatedString()  
218 -  
219 - group = stag.split("|")[0][1:]  
220 - field = stag.split("|")[1][:-1]  
221 - tag_labels[stag] = data[0]  
222 -  
223 - if not group in data_dict.keys():  
224 - data_dict[group] = {}  
225 -  
226 - if not(utils.VerifyInvalidPListCharacter(data[1])):  
227 - data_dict[group][field] = data[1].decode(encoding)  
228 - else:  
229 - data_dict[group][field] = "Invalid Character" 274 + for t in threads:
  275 + q.put(0)
230 276
231 -  
232 - # Iterate through the Data set  
233 - iterator = dataSet.GetDES().begin()  
234 - while (not iterator.equal(dataSet.GetDES().end())):  
235 - dataElement = iterator.next()  
236 -  
237 - stf.SetFile(file)  
238 - tag = dataElement.GetTag()  
239 - data = stf.ToStringPair(tag)  
240 - stag = tag.PrintAsPipeSeparatedString()  
241 -  
242 - group = stag.split("|")[0][1:]  
243 - field = stag.split("|")[1][:-1]  
244 - tag_labels[stag] = data[0]  
245 -  
246 - if not group in data_dict.keys():  
247 - data_dict[group] = {}  
248 -  
249 - if not(utils.VerifyInvalidPListCharacter(data[1])):  
250 - data_dict[group][field] = data[1].decode(encoding)  
251 - else:  
252 - data_dict[group][field] = "Invalid Character"  
253 - 277 + for t in threads:
  278 + t.join()
254 279
255 -  
256 - # ---------- Refactory --------------------------------------  
257 - data_dict['invesalius'] = {'orientation_label' : GetImageOrientationLabel(filename)} 280 + #TODO: Is this commented update necessary?
  281 + #grouper.Update()
  282 + yield grouper.GetPatientsGroups()
258 283
259 - # -------------------------------------------------------------  
260 - filepath = os.path.abspath(filename)  
261 - dict_file[filepath] = data_dict  
262 -  
263 - #---------- Verify is DICOMDir -------------------------------  
264 - is_dicom_dir = 1  
265 - try:  
266 - if (data_dict['0002']['0002'] != "1.2.840.10008.1.3.10"): #DICOMDIR  
267 - is_dicom_dir = 0  
268 - except(KeyError):  
269 - is_dicom_dir = 0  
270 -  
271 - if not(is_dicom_dir):  
272 - parser = dicom.Parser()  
273 - parser.SetDataImage(dict_file[filepath], filepath)  
274 -  
275 - dcm = dicom.Dicom()  
276 - dcm.SetParser(parser)  
277 - grouper.AddFile(dcm)  
278 284
279 -  
280 - #------- to test -------------------------------------  
281 - #main_dict = dict(  
282 - # data = dict_file,  
283 - # labels = tag_labels)  
284 -  
285 - #plistlib.writePlist(main_dict, ".//teste.plist")  
286 -  
287 - grouper.Update()  
288 -  
289 - return grouper.GetPatientsGroups()  
290 -  
291 - else:  
292 - pass  
293 - #dirpath, dirnames, filenames = os.walk(directory)  
294 - #nfiles = len(filenames)  
295 -  
296 - #counter = 0  
297 - #grouper = dicom_grouper.DicomPatientGrouper()  
298 - #q = Queue.Queue()  
299 - #l = threading.Lock()  
300 - #threads = []  
301 - #for i in xrange(cpu_count()):  
302 - # t = LoadDicom(grouper, q, l)  
303 - # t.start()  
304 - # threads.append(t)  
305 - ## Retrieve only DICOM files, splited into groups  
306 - #if recursive:  
307 - # for dirpath, dirnames, filenames in os.walk(directory):  
308 - # for name in filenames:  
309 - # filepath = os.path.join(dirpath, name)  
310 - # counter += 1  
311 - # if gui:  
312 - # yield (counter,nfiles)  
313 - # q.put(filepath)  
314 - #else:  
315 - # dirpath, dirnames, filenames = os.walk(directory)  
316 - # for name in filenames:  
317 - # filepath = str(os.path.join(dirpath, name))  
318 - # counter += 1  
319 - # if gui:  
320 - # yield (counter,nfiles)  
321 - # q.put(filepath)  
322 -  
323 - #for t in threads:  
324 - # q.put(0)  
325 -  
326 - #for t in threads:  
327 - # t.join()  
328 -  
329 - ##TODO: Is this commented update necessary?  
330 - ##grouper.Update()  
331 - #yield grouper.GetPatientsGroups()  
332 -  
333 -#def GetDicomGroups(directory, recursive=True):  
334 -# return yGetDicomGroups(directory, recursive, gui=False).next() 285 +def GetDicomGroups(directory, recursive=True):
  286 + return yGetDicomGroups(directory, recursive, gui=False).next()
335 287
336 288
337 class ProgressDicomReader: 289 class ProgressDicomReader:
@@ -364,7 +316,9 @@ class ProgressDicomReader: @@ -364,7 +316,9 @@ class ProgressDicomReader:
364 fow.SetFileName(log_path) 316 fow.SetFileName(log_path)
365 ow = vtk.vtkOutputWindow() 317 ow = vtk.vtkOutputWindow()
366 ow.SetInstance(fow) 318 ow.SetInstance(fow)
367 - 319 + print "=====>>> Progress... dicom_reader.py 367"
  320 +
  321 +
368 y = yGetDicomGroups(path, recursive) 322 y = yGetDicomGroups(path, recursive)
369 for value_progress in y: 323 for value_progress in y:
370 if not self.running: 324 if not self.running: