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Commit dfdc8ce8be5b4be448b60123632889b77ee5dee0

Authored by Thiago Franco de Moraes
1 parent 4209ef5f
Exists in master and in 56 other branches 3d_inter_style, MIPs, brush_pix, canvas_reeng, canvas_text, casmoothing_cython, clean, command-line, cython_threshold, debian_cython, editor_improvements, ff_mask, ff_mask_improv, ffill_gui, ffill_segmentation, fill_holes_auto, fixes_pre_beta5, get_pixel, import_mesh, inv3.0.1, mactoolbar, mactoolbar_bkp, manual_v3.1, mask_boolean_op, mask_boolean_op_bkp, mask_copy, mask_greatest_component, measure_canvas, measure_improvements, measure_placement_test, phoenix, region_growing_confidence, 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, user_guide_en, usp-navegador, vti, vtk6, watershed, watershed_improvements, watershed_improvements_bkp, watershed_merge, workdir, wx2.9_mac, wxgtk3, wxgtk3_b5, wxgtk3_bkp, xmartlabs-command-line

Inverting direction of projection to mip

Showing 1 changed file with 127 additions and 147 deletions   Show diff stats
invesalius/data/slice_.py
  Diff comments   View file @dfdc8ce
... ... @@ -426,14 +426,14 @@ class Slice(object):
426 426 self.buffer_slices[orientation].discard_vtk_mask()
427 427  
428 428  
429   - def GetSlices(self, orientation, slice_number, number_slices):
  429 + def GetSlices(self, orientation, slice_number, number_slices, inverted=False):
430 430 if self.buffer_slices[orientation].index == slice_number and \
431 431 self._type_projection == const.PROJECTION_NORMAL:
432 432 if self.buffer_slices[orientation].vtk_image:
433 433 image = self.buffer_slices[orientation].vtk_image
434 434 else:
435 435 n_image = self.get_image_slice(orientation, slice_number,
436   - number_slices)
  436 + number_slices, inverted)
437 437 image = converters.to_vtk(n_image, self.spacing, slice_number, orientation)
438 438 ww_wl_image = self.do_ww_wl(image)
439 439 image = self.do_colour_image(ww_wl_image)
... ... @@ -454,7 +454,7 @@ class Slice(object):
454 454 self.buffer_slices[orientation].vtk_image = image
455 455 else:
456 456 n_image = self.get_image_slice(orientation, slice_number,
457   - number_slices)
  457 + number_slices, inverted)
458 458 image = converters.to_vtk(n_image, self.spacing, slice_number, orientation)
459 459 ww_wl_image = self.do_ww_wl(image)
460 460 image = self.do_colour_image(ww_wl_image)
... ... @@ -477,7 +477,7 @@ class Slice(object):
477 477  
478 478 return final_image
479 479  
480   - def get_image_slice(self, orientation, slice_number, number_slices=1):
  480 + def get_image_slice(self, orientation, slice_number, number_slices=1, inverted=False):
481 481 if self.buffer_slices[orientation].index == slice_number \
482 482 and self.buffer_slices[orientation].image is not None:
483 483 n_image = self.buffer_slices[orientation].image
... ... @@ -486,161 +486,141 @@ class Slice(object):
486 486 if orientation == 'AXIAL':
487 487 if self._type_projection == const.PROJECTION_NORMAL:
488 488 n_image = numpy.array(self.matrix[slice_number])
489   - elif self._type_projection == const.PROJECTION_MaxIP:
490   - n_image = numpy.array(self.matrix[slice_number:
491   - slice_number+number_slices]).max(0)
492   - elif self._type_projection == const.PROJECTION_MinIP:
493   - n_image = numpy.array(self.matrix[slice_number:
494   - slice_number+number_slices]).min(0)
495   - elif self._type_projection == const.PROJECTION_MeanIP:
496   - n_image = numpy.array(self.matrix[slice_number:
497   - slice_number+number_slices]).mean(0)
498   - elif self._type_projection == const.PROJECTION_LMIP:
499   - tmp_array = numpy.array(self.matrix[slice_number:
500   - slice_number + number_slices])
501   - n_image = numpy.empty(shape=(tmp_array.shape[1],
502   - tmp_array.shape[2]),
503   - dtype=tmp_array.dtype)
504   - mips.lmip(tmp_array, 0, self.window_level, self.window_level, n_image)
505   - elif self._type_projection == const.PROJECTION_MIDA:
506   - tmp_array = numpy.array(self.matrix[slice_number:
507   - slice_number + number_slices])
508   - n_image = numpy.empty(shape=(tmp_array.shape[1],
509   - tmp_array.shape[2]),
510   - dtype=tmp_array.dtype)
511   - mips.mida(tmp_array, 0, self.window_level, self.window_level, n_image)
512   - elif self._type_projection == const.PROJECTION_CONTOUR_MIP:
513   - tmp_array = numpy.array(self.matrix[slice_number:
514   - slice_number + number_slices])
515   - n_image = numpy.empty(shape=(tmp_array.shape[1],
516   - tmp_array.shape[2]),
517   - dtype=tmp_array.dtype)
518   - mips.fast_countour_mip(tmp_array, self.n_border, 0, self.window_level,
519   - self.window_level, 0, n_image)
520   - elif self._type_projection == const.PROJECTION_CONTOUR_LMIP:
521   - tmp_array = numpy.array(self.matrix[slice_number:
522   - slice_number + number_slices])
523   - n_image = numpy.empty(shape=(tmp_array.shape[1],
524   - tmp_array.shape[2]),
525   - dtype=tmp_array.dtype)
526   - mips.fast_countour_mip(tmp_array, self.n_border, 0, self.window_level,
527   - self.window_level, 1, n_image)
528   - elif self._type_projection == const.PROJECTION_CONTOUR_MIDA:
  489 + else:
529 490 tmp_array = numpy.array(self.matrix[slice_number:
530 491 slice_number + number_slices])
531   - n_image = numpy.empty(shape=(tmp_array.shape[1],
532   - tmp_array.shape[2]),
533   - dtype=tmp_array.dtype)
534   - mips.fast_countour_mip(tmp_array, self.n_border, 0, self.window_level,
535   - self.window_level, 2, n_image)
536   - else:
537   - n_image = numpy.array(self.matrix[slice_number])
  492 + if inverted:
  493 + tmp_array = tmp_array[::-1]
  494 +
  495 + if self._type_projection == const.PROJECTION_MaxIP:
  496 + n_image = numpy.array(tmp_array).max(0)
  497 + elif self._type_projection == const.PROJECTION_MinIP:
  498 + n_image = numpy.array(tmp_array).min(0)
  499 + elif self._type_projection == const.PROJECTION_MeanIP:
  500 + n_image = numpy.array(tmp_array).mean(0)
  501 + elif self._type_projection == const.PROJECTION_LMIP:
  502 + n_image = numpy.empty(shape=(tmp_array.shape[1],
  503 + tmp_array.shape[2]),
  504 + dtype=tmp_array.dtype)
  505 + mips.lmip(tmp_array, 0, self.window_level, self.window_level, n_image)
  506 + elif self._type_projection == const.PROJECTION_MIDA:
  507 + n_image = numpy.empty(shape=(tmp_array.shape[1],
  508 + tmp_array.shape[2]),
  509 + dtype=tmp_array.dtype)
  510 + mips.mida(tmp_array, 0, self.window_level, self.window_level, n_image)
  511 + elif self._type_projection == const.PROJECTION_CONTOUR_MIP:
  512 + n_image = numpy.empty(shape=(tmp_array.shape[1],
  513 + tmp_array.shape[2]),
  514 + dtype=tmp_array.dtype)
  515 + mips.fast_countour_mip(tmp_array, self.n_border, 0, self.window_level,
  516 + self.window_level, 0, n_image)
  517 + elif self._type_projection == const.PROJECTION_CONTOUR_LMIP:
  518 + n_image = numpy.empty(shape=(tmp_array.shape[1],
  519 + tmp_array.shape[2]),
  520 + dtype=tmp_array.dtype)
  521 + mips.fast_countour_mip(tmp_array, self.n_border, 0, self.window_level,
  522 + self.window_level, 1, n_image)
  523 + elif self._type_projection == const.PROJECTION_CONTOUR_MIDA:
  524 + n_image = numpy.empty(shape=(tmp_array.shape[1],
  525 + tmp_array.shape[2]),
  526 + dtype=tmp_array.dtype)
  527 + mips.fast_countour_mip(tmp_array, self.n_border, 0, self.window_level,
  528 + self.window_level, 2, n_image)
  529 + else:
  530 + n_image = numpy.array(self.matrix[slice_number])
538 531  
539 532 elif orientation == 'CORONAL':
540 533 if self._type_projection == const.PROJECTION_NORMAL:
541 534 n_image = numpy.array(self.matrix[..., slice_number, ...])
542   - elif self._type_projection == const.PROJECTION_MaxIP:
543   - n_image = numpy.array(self.matrix[..., slice_number:
544   - slice_number+number_slices, ...]).max(1)
545   - elif self._type_projection == const.PROJECTION_MinIP:
546   - n_image = numpy.array(self.matrix[..., slice_number:
547   - slice_number+number_slices, ...]).min(1)
548   - elif self._type_projection == const.PROJECTION_MeanIP:
549   - n_image = numpy.array(self.matrix[..., slice_number:
550   - slice_number+number_slices, ...]).mean(1)
551   - elif self._type_projection == const.PROJECTION_LMIP:
552   - tmp_array = numpy.array(self.matrix[..., slice_number:
553   - slice_number + number_slices, ...])
554   - n_image = numpy.empty(shape=(tmp_array.shape[0],
555   - tmp_array.shape[2]),
556   - dtype=tmp_array.dtype)
557   - mips.lmip(tmp_array, 1, self.window_level, self.window_level, n_image)
558   - elif self._type_projection == const.PROJECTION_MIDA:
559   - tmp_array = numpy.array(self.matrix[..., slice_number:
560   - slice_number + number_slices, ...])
561   - n_image = numpy.empty(shape=(tmp_array.shape[0],
562   - tmp_array.shape[2]),
563   - dtype=tmp_array.dtype)
564   - mips.mida(tmp_array, 1, self.window_level, self.window_level, n_image)
565   - elif self._type_projection == const.PROJECTION_CONTOUR_MIP:
566   - tmp_array = numpy.array(self.matrix[..., slice_number:
567   - slice_number + number_slices, ...])
568   - n_image = numpy.empty(shape=(tmp_array.shape[0],
569   - tmp_array.shape[2]),
570   - dtype=tmp_array.dtype)
571   - mips.fast_countour_mip(tmp_array, self.n_border, 1, self.window_level,
572   - self.window_level, 0, n_image)
573   - elif self._type_projection == const.PROJECTION_CONTOUR_LMIP:
574   - tmp_array = numpy.array(self.matrix[..., slice_number:
575   - slice_number + number_slices, ...])
576   - n_image = numpy.empty(shape=(tmp_array.shape[0],
577   - tmp_array.shape[2]),
578   - dtype=tmp_array.dtype)
579   - mips.fast_countour_mip(tmp_array, self.n_border, 1, self.window_level,
580   - self.window_level, 1, n_image)
581   - elif self._type_projection == const.PROJECTION_CONTOUR_MIDA:
582   - tmp_array = numpy.array(self.matrix[..., slice_number:
583   - slice_number + number_slices, ...])
584   - n_image = numpy.empty(shape=(tmp_array.shape[0],
585   - tmp_array.shape[2]),
586   - dtype=tmp_array.dtype)
587   - mips.fast_countour_mip(tmp_array, self.n_border, 1, self.window_level,
588   - self.window_level, 2, n_image)
589 535 else:
590   - n_image = numpy.array(self.matrix[..., slice_number, ...])
  536 + #if slice_number == 0:
  537 + #slice_number = 1
  538 + #if slice_number - number_slices < 0:
  539 + #number_slices = slice_number
  540 + tmp_array = numpy.array(self.matrix[..., slice_number: slice_number + number_slices, ...])
  541 + if inverted:
  542 + tmp_array = tmp_array[..., ::-1, ...]
  543 + if self._type_projection == const.PROJECTION_MaxIP:
  544 + n_image = numpy.array(tmp_array).max(1)
  545 + elif self._type_projection == const.PROJECTION_MinIP:
  546 + n_image = numpy.array(tmp_array).min(1)
  547 + elif self._type_projection == const.PROJECTION_MeanIP:
  548 + n_image = numpy.array(tmp_array).mean(1)
  549 + elif self._type_projection == const.PROJECTION_LMIP:
  550 + n_image = numpy.empty(shape=(tmp_array.shape[0],
  551 + tmp_array.shape[2]),
  552 + dtype=tmp_array.dtype)
  553 + mips.lmip(tmp_array, 1, self.window_level, self.window_level, n_image)
  554 + elif self._type_projection == const.PROJECTION_MIDA:
  555 + n_image = numpy.empty(shape=(tmp_array.shape[0],
  556 + tmp_array.shape[2]),
  557 + dtype=tmp_array.dtype)
  558 + mips.mida(tmp_array, 1, self.window_level, self.window_level, n_image)
  559 + elif self._type_projection == const.PROJECTION_CONTOUR_MIP:
  560 + n_image = numpy.empty(shape=(tmp_array.shape[0],
  561 + tmp_array.shape[2]),
  562 + dtype=tmp_array.dtype)
  563 + mips.fast_countour_mip(tmp_array, self.n_border, 1, self.window_level,
  564 + self.window_level, 0, n_image)
  565 + elif self._type_projection == const.PROJECTION_CONTOUR_LMIP:
  566 + n_image = numpy.empty(shape=(tmp_array.shape[0],
  567 + tmp_array.shape[2]),
  568 + dtype=tmp_array.dtype)
  569 + mips.fast_countour_mip(tmp_array, self.n_border, 1, self.window_level,
  570 + self.window_level, 1, n_image)
  571 + elif self._type_projection == const.PROJECTION_CONTOUR_MIDA:
  572 + n_image = numpy.empty(shape=(tmp_array.shape[0],
  573 + tmp_array.shape[2]),
  574 + dtype=tmp_array.dtype)
  575 + mips.fast_countour_mip(tmp_array, self.n_border, 1, self.window_level,
  576 + self.window_level, 2, n_image)
  577 + else:
  578 + n_image = numpy.array(self.matrix[..., slice_number, ...])
591 579 elif orientation == 'SAGITAL':
592 580 if self._type_projection == const.PROJECTION_NORMAL:
593 581 n_image = numpy.array(self.matrix[..., ..., slice_number])
594   - elif self._type_projection == const.PROJECTION_MaxIP:
595   - n_image = numpy.array(self.matrix[..., ..., slice_number:
596   - slice_number+number_slices]).max(2)
597   - elif self._type_projection == const.PROJECTION_MinIP:
598   - n_image = numpy.array(self.matrix[..., ..., slice_number:
599   - slice_number+number_slices]).min(2)
600   - elif self._type_projection == const.PROJECTION_MeanIP:
601   - n_image = numpy.array(self.matrix[..., ..., slice_number:
602   - slice_number+number_slices]).mean(2)
603   - elif self._type_projection == const.PROJECTION_LMIP:
604   - tmp_array = numpy.array(self.matrix[..., ...,
605   - slice_number: slice_number + number_slices])
606   - n_image = numpy.empty(shape=(tmp_array.shape[0],
607   - tmp_array.shape[1]),
608   - dtype=tmp_array.dtype)
609   - mips.lmip(tmp_array, 2, self.window_level, self.window_level, n_image)
610   - elif self._type_projection == const.PROJECTION_MIDA:
611   - tmp_array = numpy.array(self.matrix[..., ...,
612   - slice_number: slice_number + number_slices])
613   - n_image = numpy.empty(shape=(tmp_array.shape[0],
614   - tmp_array.shape[1]),
615   - dtype=tmp_array.dtype)
616   - mips.mida(tmp_array, 2, self.window_level, self.window_level, n_image)
617   -
618   - elif self._type_projection == const.PROJECTION_CONTOUR_MIP:
619   - tmp_array = numpy.array(self.matrix[..., ...,
620   - slice_number: slice_number + number_slices])
621   - n_image = numpy.empty(shape=(tmp_array.shape[0],
622   - tmp_array.shape[1]),
623   - dtype=tmp_array.dtype)
624   - mips.fast_countour_mip(tmp_array, self.n_border, 2, self.window_level,
625   - self.window_level, 0, n_image)
626   - elif self._type_projection == const.PROJECTION_CONTOUR_LMIP:
627   - tmp_array = numpy.array(self.matrix[..., ...,
628   - slice_number: slice_number + number_slices])
629   - n_image = numpy.empty(shape=(tmp_array.shape[0],
630   - tmp_array.shape[1]),
631   - dtype=tmp_array.dtype)
632   - mips.fast_countour_mip(tmp_array, self.n_border, 2, self.window_level,
633   - self.window_level, 1, n_image)
634   - elif self._type_projection == const.PROJECTION_CONTOUR_MIDA:
  582 + else:
635 583 tmp_array = numpy.array(self.matrix[..., ...,
636 584 slice_number: slice_number + number_slices])
637   - n_image = numpy.empty(shape=(tmp_array.shape[0],
638   - tmp_array.shape[1]),
639   - dtype=tmp_array.dtype)
640   - mips.fast_countour_mip(tmp_array, self.n_border, 2, self.window_level,
641   - self.window_level, 2, n_image)
642   - else:
643   - n_image = numpy.array(self.matrix[..., ..., slice_number])
  585 + if inverted:
  586 + tmp_array = tmp_array[..., ..., ::-1]
  587 + if self._type_projection == const.PROJECTION_MaxIP:
  588 + n_image = numpy.array(tmp_array).max(2)
  589 + elif self._type_projection == const.PROJECTION_MinIP:
  590 + n_image = numpy.array(tmp_array).min(2)
  591 + elif self._type_projection == const.PROJECTION_MeanIP:
  592 + n_image = numpy.array(tmp_array).mean(2)
  593 + elif self._type_projection == const.PROJECTION_LMIP:
  594 + n_image = numpy.empty(shape=(tmp_array.shape[0],
  595 + tmp_array.shape[1]),
  596 + dtype=tmp_array.dtype)
  597 + mips.lmip(tmp_array, 2, self.window_level, self.window_level, n_image)
  598 + elif self._type_projection == const.PROJECTION_MIDA:
  599 + n_image = numpy.empty(shape=(tmp_array.shape[0],
  600 + tmp_array.shape[1]),
  601 + dtype=tmp_array.dtype)
  602 + mips.mida(tmp_array, 2, self.window_level, self.window_level, n_image)
  603 +
  604 + elif self._type_projection == const.PROJECTION_CONTOUR_MIP:
  605 + n_image = numpy.empty(shape=(tmp_array.shape[0],
  606 + tmp_array.shape[1]),
  607 + dtype=tmp_array.dtype)
  608 + mips.fast_countour_mip(tmp_array, self.n_border, 2, self.window_level,
  609 + self.window_level, 0, n_image)
  610 + elif self._type_projection == const.PROJECTION_CONTOUR_LMIP:
  611 + n_image = numpy.empty(shape=(tmp_array.shape[0],
  612 + tmp_array.shape[1]),
  613 + dtype=tmp_array.dtype)
  614 + mips.fast_countour_mip(tmp_array, self.n_border, 2, self.window_level,
  615 + self.window_level, 1, n_image)
  616 + elif self._type_projection == const.PROJECTION_CONTOUR_MIDA:
  617 + n_image = numpy.empty(shape=(tmp_array.shape[0],
  618 + tmp_array.shape[1]),
  619 + dtype=tmp_array.dtype)
  620 + mips.fast_countour_mip(tmp_array, self.n_border, 2, self.window_level,
  621 + self.window_level, 2, n_image)
  622 + else:
  623 + n_image = numpy.array(self.matrix[..., ..., slice_number])
644 624 return n_image
645 625  
646 626 def get_mask_slice(self, orientation, slice_number):
... ...