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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): @@ -426,14 +426,14 @@ class Slice(object):
426 self.buffer_slices[orientation].discard_vtk_mask() 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 if self.buffer_slices[orientation].index == slice_number and \ 430 if self.buffer_slices[orientation].index == slice_number and \
431 self._type_projection == const.PROJECTION_NORMAL: 431 self._type_projection == const.PROJECTION_NORMAL:
432 if self.buffer_slices[orientation].vtk_image: 432 if self.buffer_slices[orientation].vtk_image:
433 image = self.buffer_slices[orientation].vtk_image 433 image = self.buffer_slices[orientation].vtk_image
434 else: 434 else:
435 n_image = self.get_image_slice(orientation, slice_number, 435 n_image = self.get_image_slice(orientation, slice_number,
436 - number_slices) 436 + number_slices, inverted)
437 image = converters.to_vtk(n_image, self.spacing, slice_number, orientation) 437 image = converters.to_vtk(n_image, self.spacing, slice_number, orientation)
438 ww_wl_image = self.do_ww_wl(image) 438 ww_wl_image = self.do_ww_wl(image)
439 image = self.do_colour_image(ww_wl_image) 439 image = self.do_colour_image(ww_wl_image)
@@ -454,7 +454,7 @@ class Slice(object): @@ -454,7 +454,7 @@ class Slice(object):
454 self.buffer_slices[orientation].vtk_image = image 454 self.buffer_slices[orientation].vtk_image = image
455 else: 455 else:
456 n_image = self.get_image_slice(orientation, slice_number, 456 n_image = self.get_image_slice(orientation, slice_number,
457 - number_slices) 457 + number_slices, inverted)
458 image = converters.to_vtk(n_image, self.spacing, slice_number, orientation) 458 image = converters.to_vtk(n_image, self.spacing, slice_number, orientation)
459 ww_wl_image = self.do_ww_wl(image) 459 ww_wl_image = self.do_ww_wl(image)
460 image = self.do_colour_image(ww_wl_image) 460 image = self.do_colour_image(ww_wl_image)
@@ -477,7 +477,7 @@ class Slice(object): @@ -477,7 +477,7 @@ class Slice(object):
477 477
478 return final_image 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 if self.buffer_slices[orientation].index == slice_number \ 481 if self.buffer_slices[orientation].index == slice_number \
482 and self.buffer_slices[orientation].image is not None: 482 and self.buffer_slices[orientation].image is not None:
483 n_image = self.buffer_slices[orientation].image 483 n_image = self.buffer_slices[orientation].image
@@ -486,161 +486,141 @@ class Slice(object): @@ -486,161 +486,141 @@ class Slice(object):
486 if orientation == 'AXIAL': 486 if orientation == 'AXIAL':
487 if self._type_projection == const.PROJECTION_NORMAL: 487 if self._type_projection == const.PROJECTION_NORMAL:
488 n_image = numpy.array(self.matrix[slice_number]) 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 tmp_array = numpy.array(self.matrix[slice_number: 490 tmp_array = numpy.array(self.matrix[slice_number:
530 slice_number + number_slices]) 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 elif orientation == 'CORONAL': 532 elif orientation == 'CORONAL':
540 if self._type_projection == const.PROJECTION_NORMAL: 533 if self._type_projection == const.PROJECTION_NORMAL:
541 n_image = numpy.array(self.matrix[..., slice_number, ...]) 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 else: 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 elif orientation == 'SAGITAL': 579 elif orientation == 'SAGITAL':
592 if self._type_projection == const.PROJECTION_NORMAL: 580 if self._type_projection == const.PROJECTION_NORMAL:
593 n_image = numpy.array(self.matrix[..., ..., slice_number]) 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 tmp_array = numpy.array(self.matrix[..., ..., 583 tmp_array = numpy.array(self.matrix[..., ...,
636 slice_number: slice_number + number_slices]) 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 return n_image 624 return n_image
645 625
646 def get_mask_slice(self, orientation, slice_number): 626 def get_mask_slice(self, orientation, slice_number):