Commit 61d6ebfa72727b21617892f7b14ef792c3bcb050
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d6839add
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ENH: Turned thread support in importation
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158 additions
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203 deletions
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invesalius/control.py
... | ... | @@ -120,12 +120,13 @@ class Controller(): |
120 | 120 | answer = dialog.SaveChangesDialog2(filename) |
121 | 121 | if answer: |
122 | 122 | self.ShowDialogSaveProject() |
123 | - | |
124 | 123 | # Import project |
125 | 124 | dirpath = dialog.ShowImportDirDialog() |
126 | 125 | if dirpath and not os.listdir(dirpath): |
126 | + print "IFFFFFFFfff" | |
127 | 127 | dialog.ImportEmptyDirectory(dirpath) |
128 | 128 | elif dirpath: |
129 | + print "ELSE..........." | |
129 | 130 | self.StartImportPanel(dirpath) |
130 | 131 | ps.Publisher().sendMessage("Load data to import panel", dirpath) |
131 | 132 | ... | ... |
invesalius/reader/dicom_reader.py
... | ... | @@ -79,60 +79,132 @@ def SortFiles(filelist, dicom): |
79 | 79 | |
80 | 80 | return filelist |
81 | 81 | |
82 | -""" | |
82 | +tag_labels = {} | |
83 | +main_dict = {} | |
84 | +dict_file = {} | |
85 | + | |
83 | 86 | class LoadDicom(threading.Thread): |
87 | + | |
84 | 88 | def __init__(self, grouper, q, l): |
85 | 89 | threading.Thread.__init__(self) |
86 | 90 | self.grouper = grouper |
87 | 91 | self.q = q |
88 | 92 | self.l = l |
93 | + | |
89 | 94 | def run(self): |
95 | + | |
90 | 96 | grouper = self.grouper |
91 | 97 | q = self.q |
98 | + | |
92 | 99 | while 1: |
100 | + | |
93 | 101 | filepath = q.get() |
94 | 102 | if not filepath: |
95 | 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 | 210 | def GetImageOrientationLabel(filename): |
... | ... | @@ -158,180 +230,60 @@ def GetImageOrientationLabel(filename): |
158 | 230 | else: |
159 | 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 | 236 | Return all full paths to DICOM files inside given directory. |
166 | 237 | """ |
167 | - | |
168 | 238 | nfiles = 0 |
169 | 239 | # Find total number of files |
170 | 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 | 289 | class ProgressDicomReader: |
... | ... | @@ -364,7 +316,9 @@ class ProgressDicomReader: |
364 | 316 | fow.SetFileName(log_path) |
365 | 317 | ow = vtk.vtkOutputWindow() |
366 | 318 | ow.SetInstance(fow) |
367 | - | |
319 | + print "=====>>> Progress... dicom_reader.py 367" | |
320 | + | |
321 | + | |
368 | 322 | y = yGetDicomGroups(path, recursive) |
369 | 323 | for value_progress in y: |
370 | 324 | if not self.running: | ... | ... |