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Commit 0759123d5d69d55174d6a970b55c49c15dc0a949

Authored by tfmoraes
1 parent 4838dfee
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: Improvements in mask threshold, like use of buffers, better use of numpy.arrays and some fixes.

Showing 1 changed file with 61 additions and 56 deletions   Show diff stats
invesalius/data/slice_.py
  Diff comments   View file @0759123
... ... @@ -184,6 +184,7 @@ class Slice(object):
184 184 self.CreateMask(name=mask_name, threshold_range=thresh, colour =colour)
185 185 self.SetMaskColour(self.current_mask.index, self.current_mask.colour)
186 186 self.SelectCurrentMask(self.current_mask.index)
  187 + ps.Publisher().sendMessage('Reload actual slice')
187 188  
188 189 def __select_current_mask(self, pubsub_evt):
189 190 mask_index = pubsub_evt.data
... ... @@ -259,12 +260,15 @@ class Slice(object):
259 260 #---------------------------------------------------------------------------
260 261  
261 262 def GetSlices(self, orientation, slice_number):
  263 + print "Getting slice", self.buffer_slices[orientation][0], slice_number
262 264 if self.buffer_slices[orientation][0] == slice_number:
263   - print "From buffer"
264 265 image = self.buffer_slices[orientation][1]
265   - n_mask = self.buffer_slices[orientation][2]
266   - mask = iu.to_vtk(n_mask, self.spacing, slice_number, orientation)
267   - final_image = self.do_blend(image, self.do_colour_mask(mask))
  266 + if self.current_mask and self.current_mask.is_shown:
  267 + n_mask = self.buffer_slices[orientation][2]
  268 + mask = iu.to_vtk(n_mask, self.spacing, slice_number, orientation)
  269 + final_image = self.do_blend(image, self.do_colour_mask(mask))
  270 + else:
  271 + final_image = image
268 272 else:
269 273 n_image = self.GetImageSlice(orientation, slice_number)
270 274 image = iu.to_vtk(n_image, self.spacing, slice_number, orientation)
... ... @@ -285,39 +289,49 @@ class Slice(object):
285 289 return final_image
286 290  
287 291 def GetImageSlice(self, orientation, slice_number):
288   - if orientation == 'AXIAL':
289   - n_image = numpy.array(self.matrix[slice_number])
290   - elif orientation == 'CORONAL':
291   - n_image = numpy.array(self.matrix[..., slice_number, ...])
292   - elif orientation == 'SAGITAL':
293   - n_image = numpy.array(self.matrix[..., ..., slice_number])
  292 + if self.buffer_slices[orientation] == slice_number:
  293 + n_image = self.buffer_slices[orientation][3]
  294 + else:
  295 + if orientation == 'AXIAL':
  296 + n_image = numpy.array(self.matrix[slice_number])
  297 + elif orientation == 'CORONAL':
  298 + n_image = numpy.array(self.matrix[..., slice_number, ...])
  299 + elif orientation == 'SAGITAL':
  300 + n_image = numpy.array(self.matrix[..., ..., slice_number])
294 301 return n_image
295 302  
296 303 def GetMaskSlice(self, orientation, slice_number):
297   - slice_number += 1
  304 + """
  305 + It gets the from actual mask the given slice from given orientation
  306 + """
  307 +
  308 + # It's necessary because the first position for each dimension from
  309 + # mask matrix is used as flags to control if the mask in the
  310 + # slice_number position has been generated.
  311 + n = slice_number + 1
298 312 if orientation == 'AXIAL':
299   - if self.current_mask.matrix[slice_number, 0, 0] == 0:
300   - self.current_mask.matrix[slice_number, 1:, 1:] = \
  313 + if self.current_mask.matrix[n, 0, 0] == 0:
  314 + self.current_mask.matrix[n, 1:, 1:] = \
301 315 self.do_threshold_to_a_slice(self.GetImageSlice(orientation,
302 316 slice_number))
303   - self.current_mask.matrix[slice_number, 0, 0] = 1
304   - n_mask = numpy.array(self.current_mask.matrix[slice_number])
  317 + self.current_mask.matrix[n, 0, 0] = 1
  318 + n_mask = numpy.array(self.current_mask.matrix[n, 1:, 1:])
305 319  
306 320 elif orientation == 'CORONAL':
307   - if self.current_mask.matrix[0, slice_number, 0] == 0:
308   - self.current_mask.matrix[1:, slice_number, 1:] = \
  321 + if self.current_mask.matrix[0, n, 0] == 0:
  322 + self.current_mask.matrix[1:, n, 1:] = \
309 323 self.do_threshold_to_a_slice(self.GetImageSlice(orientation,
310 324 slice_number))
311   - self.current_mask.matrix[0, slice_number, 0] = 1
312   - n_mask = numpy.array(self.current_mask.matrix[..., slice_number, ...])
  325 + self.current_mask.matrix[0, n, 0] = 1
  326 + n_mask = numpy.array(self.current_mask.matrix[1:, n, 1:])
313 327  
314 328 elif orientation == 'SAGITAL':
315   - if self.current_mask.matrix[0, 0, slice_number] == 0:
316   - self.current_mask.matrix[1:, 1:, slice_number] = \
  329 + if self.current_mask.matrix[0, 0, n] == 0:
  330 + self.current_mask.matrix[1:, 1:, n] = \
317 331 self.do_threshold_to_a_slice(self.GetImageSlice(orientation,
318 332 slice_number))
319   - self.current_mask.matrix[0, 0, slice_number] = 1
320   - n_mask = numpy.array(self.current_mask.matrix[..., ..., slice_number])
  333 + self.current_mask.matrix[0, 0, n] = 1
  334 + n_mask = numpy.array(self.current_mask.matrix[1:, 1:, n])
321 335 return n_mask
322 336  
323 337 def GetNumberOfSlices(self, orientation):
... ... @@ -401,9 +415,8 @@ class Slice(object):
401 415 else:
402 416 print "Only one slice"
403 417 slice_ = self.buffer_slices[orientation][3]
404   - m = numpy.zeros(slice_.shape, self.current_mask.matrix.dtype)
405   - m[numpy.logical_and(slice_ >= thresh_min,slice_ <= thresh_max)] = 255
406   - self.buffer_slices[orientation][2] = m
  418 + self.buffer_slices[orientation][2][:] = 0
  419 + self.buffer_slices[orientation][2][numpy.logical_and(slice_ >= thresh_min,slice_ <= thresh_max)] = 255
407 420  
408 421 # Update viewer
409 422 #ps.Publisher().sendMessage('Update slice viewer')
... ... @@ -425,12 +438,10 @@ class Slice(object):
425 438 proj = Project()
426 439 proj.mask_dict[index].is_shown = value
427 440 if (index == self.current_mask.index):
428   - if value:
429   - self.blend_filter.SetOpacity(1, self.current_mask.opacity)
430   - else:
431   - self.blend_filter.SetOpacity(1, 0)
432   - self.blend_filter.Update()
433   - ps.Publisher().sendMessage('Update slice viewer')
  441 + self.buffer_slices = {"AXIAL": [-1, None, None],
  442 + "CORONAL": [-1,None, None],
  443 + "SAGITAL": [-1, None, None]}
  444 + ps.Publisher().sendMessage('Reload actual slice')
434 445 #---------------------------------------------------------------------------
435 446 def ErasePixel(self, position):
436 447 "Delete pixel, based on x, y and z position coordinates."
... ... @@ -478,33 +489,27 @@ class Slice(object):
478 489 #if index != self.current_mask.index:
479 490 print "SelectCurrentMask"
480 491 print "index:", index
481   - if self.current_mask and self.blend_filter and index > -1:
482   - proj = Project()
483   - future_mask = proj.GetMask(index)
484   - future_mask.is_shown = True
485   - self.current_mask = future_mask
486   -
487   - colour = future_mask.colour
488   - #index = future_mask.index
489   - print index
490   - self.SetMaskColour(index, colour, update=False)
  492 + proj = Project()
  493 + future_mask = proj.GetMask(index)
  494 + future_mask.is_shown = True
  495 + self.current_mask = future_mask
491 496  
492   - imagedata = future_mask.imagedata
493   - self.img_colours_mask.SetInput(imagedata)
  497 + colour = future_mask.colour
  498 + #index = future_mask.index
  499 + print index
  500 + self.SetMaskColour(index, colour, update=False)
494 501  
495   - if self.current_mask.is_shown:
496   - self.blend_filter.SetOpacity(1, self.current_mask.opacity)
497   - else:
498   - self.blend_filter.SetOpacity(1, 0)
499   - self.blend_filter.Update()
  502 + self.buffer_slices = {"AXIAL": [-1, None, None],
  503 + "CORONAL": [-1,None, None],
  504 + "SAGITAL": [-1, None, None]}
500 505  
501   - ps.Publisher().sendMessage('Set mask threshold in notebook',
502   - (index,
503   - self.current_mask.threshold_range))
504   - ps.Publisher().sendMessage('Set threshold values in gradient',
505   - self.current_mask.threshold_range)
506   - ps.Publisher().sendMessage('Select mask name in combo', index)
507   - ps.Publisher().sendMessage('Update slice viewer')
  506 + ps.Publisher().sendMessage('Set mask threshold in notebook',
  507 + (index,
  508 + self.current_mask.threshold_range))
  509 + ps.Publisher().sendMessage('Set threshold values in gradient',
  510 + self.current_mask.threshold_range)
  511 + ps.Publisher().sendMessage('Select mask name in combo', index)
  512 + ps.Publisher().sendMessage('Update slice viewer')
508 513 #---------------------------------------------------------------------------
509 514  
510 515 def CreateSurfaceFromIndex(self, pubsub_evt):
... ...