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Commit 6dc42bf885717de6f176ffcbe092060f51c06948

Authored by tfmoraes
1 parent 69aa6af4
Exists in master and in 5 other branches beta3, beta4, inv3.0.1, usp-navegador, wxgtk3_b5

Handling orientations in analyze files and storing it in memmap

Showing 2 changed files with 47 additions and 3 deletions   Show diff stats
invesalius/control.py
  Diff comments   View file @6dc42bf
... ... @@ -19,8 +19,8 @@
19 19 import math
20 20 import os
21 21 import plistlib
22   -import tempfile
23 22  
  23 +import numpy
24 24 import wx.lib.pubsub as ps
25 25  
26 26 import constants as const
... ... @@ -386,12 +386,16 @@ class Controller():
386 386 proj.SetAcquisitionModality("MRI")
387 387 #TODO: Verify if all Analyse are in AXIAL orientation
388 388  
389   - if not header['orient']:
  389 + # To get Z, X, Y (used by InVesaliu), not X, Y, Z
  390 + matrix, matrix_filename = utils.analyze2mmap(imagedata)
  391 + if header['orient'] == 0:
390 392 proj.original_orientation = const.AXIAL
391 393 elif header['orient'] == 1:
392 394 proj.original_orientation = const.CORONAL
393 395 elif header['orient'] == 2:
394 396 proj.original_orientation = const.SAGITAL
  397 + else:
  398 + proj.original_orientation = const.SAGITAL
395 399  
396 400 proj.threshold_range = (header['glmin'],
397 401 header['glmax'])
... ... @@ -399,7 +403,8 @@ class Controller():
399 403 proj.level = (0.5 * (proj.threshold_range[1] + proj.threshold_range[0]))
400 404  
401 405 self.Slice = sl.Slice()
402   - self.Slice.matrix = imagedata.get_data().swapaxes(0, 2)
  406 + self.Slice.matrix = matrix
  407 + self.Slice.matrix_filename = matrix_filename
403 408  
404 409 self.Slice.window_level = proj.level
405 410 self.Slice.window_width = proj.window
... ...
invesalius/data/imagedata_utils.py
  Diff comments   View file @6dc42bf
... ... @@ -507,6 +507,45 @@ def dcm2memmap(files, slice_size, orientation):
507 507  
508 508 return matrix, scalar_range, temp_file
509 509  
  510 +def analyze2mmap(analyze):
  511 + data = analyze.get_data()
  512 + header = analyze.get_header()
  513 + temp_file = tempfile.mktemp()
  514 +
  515 + # Sagital
  516 + if header['orient'] == 2:
  517 + print "Orientation Sagital"
  518 + shape = tuple([data.shape[i] for i in (1, 2, 0)])
  519 + matrix = numpy.memmap(temp_file, mode='w+', dtype=data.dtype, shape=shape)
  520 + for n, slice in enumerate(data):
  521 + matrix[:,:, n] = slice
  522 +
  523 + # Coronal
  524 + elif header['orient'] == 1:
  525 + print "Orientation coronal"
  526 + shape = tuple([data.shape[i] for i in (1, 0, 2)])
  527 + matrix = numpy.memmap(temp_file, mode='w+', dtype=data.dtype, shape=shape)
  528 + for n, slice in enumerate(data):
  529 + matrix[:,n,:] = slice
  530 +
  531 + # AXIAL
  532 + elif header['orient'] == 0:
  533 + print "no orientation"
  534 + shape = tuple([data.shape[i] for i in (0, 1, 2)])
  535 + matrix = numpy.memmap(temp_file, mode='w+', dtype=data.dtype, shape=shape)
  536 + for n, slice in enumerate(data):
  537 + matrix[n] = slice
  538 +
  539 + else:
  540 + print "Orientation Sagital"
  541 + shape = tuple([data.shape[i] for i in (1, 2, 0)])
  542 + matrix = numpy.memmap(temp_file, mode='w+', dtype=data.dtype, shape=shape)
  543 + for n, slice in enumerate(data):
  544 + matrix[:,:, n] = slice
  545 +
  546 + matrix.flush()
  547 + return matrix, temp_file
  548 +
510 549 def to_vtk(n_array, spacing, slice_number, orientation):
511 550 try:
512 551 dz, dy, dx = n_array.shape
... ...