Merge branch 'master' into brightness-control

* master:
  Implements MTsat function (#1672)
  Keep intermediate temp folder by default (#1694)
  sct_deepseg_sc - Issue when input is .nii instead of .nii.gz (#1634, #1659)
  sct_image: remove file removal kludge (#1688) (#1705)
  Concatenate string to keep previously assigned subtitle field (fixes #1690) (#1692)
  Enable input file with label at a specific disc (#1698)

# Conflicts:
#	spinalcordtoolbox/gui/sagittal.py

scripts/msct_register.py

@@ -38,7 +38,7 @@ def register_slicewise(fname_src,
                         paramreg=None,
                         ants_registration_params=None,
                         path_qc='./',
-                        remove_temp_files=1,
+                        remove_temp_files=0,
                         verbose=0):
 
     # create temporary folder

scripts/sct_compute_mtsat.py

@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+# -*- coding: utf-8
+#########################################################################################
+#
+# Compute MT saturation map and T1 map from a PD-weigthed, a T1-weighted and MT-weighted FLASH images
+#
+# Reference paper:
+#    Helms G, Dathe H, Kallenberg K, Dechent P. High-resolution maps of magnetization transfer with inherent correction
+#    for RF inhomogeneity and T1 relaxation obtained from 3D FLASH MRI. Magn Reson Med 2008;60(6):1396-1407.
+
+# ---------------------------------------------------------------------------------------
+# Copyright (c) 2018 Polytechnique Montreal <www.neuro.polymtl.ca>
+# Author: Julien Cohen-Adad
+#
+# About the license: see the file LICENSE.TXT
+#########################################################################################
+
+
+import argparse
+
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        description='Compute MTsat and T1map.'
+                    'Reference: Helms G, Dathe H, Kallenberg K, Dechent P. High-resolution maps of magnetization '
+                    'transfer with inherent correction for RF inhomogeneity and T1 relaxation obtained from 3D FLASH '
+                    'MRI. Magn Reson Med 2008;60(6):1396-1407.')
+    parser.add_argument("-mt",
+                        help="Image with MT_ON",
+                        required=True)
+    parser.add_argument("-pd",
+                        help="Image PD weighted (typically, the MT_OFF)",
+                        required=True)
+    parser.add_argument("-t1",
+                        help="Image T1-weighted",
+                        required=True)
+    parser.add_argument("-trmt",
+                        help="TR [in ms] for mt image.",
+                        type=float,
+                        required=True)
+    parser.add_argument("-trpd",
+                        help="TR [in ms] for pd image.",
+                        type=float,
+                        required=True)
+    parser.add_argument("-trt1",
+                        help="TR [in ms] for t1 image.",
+                        type=float,
+                        required=True)
+    parser.add_argument("-famt",
+                        help="Flip angle [in deg] for mt image.",
+                        type=float,
+                        required=True)
+    parser.add_argument("-fapd",
+                        help="Flip angle [in deg] for pd image.",
+                        type=float,
+                        required=True)
+    parser.add_argument("-fat1",
+                        help="Flip angle [in deg] for t1 image.",
+                        type=float,
+                        required=True)
+    parser.add_argument("-b1map",
+                        help="B1 map",
+                        default=None)
+    parser.add_argument("-omtsat",
+                        help="Output file for MTsat. Default is mtsat.nii.gz",
+                        default=None)
+    parser.add_argument("-ot1map",
+                        help="Output file for T1map. Default is t1map.nii.gz",
+                        default=None)
+    parser.add_argument("-v",
+                        help="Verbose: 0 = no verbosity, 1 = verbose (default).",
+                        choices=('0', '1'),
+                        type=int,
+                        default=1)
+    return parser
+
+
+def run_main(args):
+    import sct_utils as sct
+    from spinalcordtoolbox.mtsat import mtsat
+
+    sct.start_stream_logger()
+
+    fname_mtsat, fname_t1map = mtsat.compute_mtsat_from_file(
+        args.mt, args.pd, args.t1, args.trmt, args.trpd, args.trt1, args.famt, args.fapd, args.fat1,
+        fname_b1map=args.b1map, fname_mtsat=args.omtsat, fname_t1map=args.ot1map, verbose=1)
+
+    sct.display_viewer_syntax([fname_mtsat, fname_t1map],
+                              colormaps=['gray', 'gray'],
+                              minmax=['-10,10', '0, 3'],
+                              opacities=['1', '1'],
+                              verbose=args.v)
+
+
+if __name__ == '__main__':
+    parser = get_parser()
+    arguments = parser.parse_args()
+    run_main(arguments)

scripts/sct_deepseg_sc.py

@@ -99,7 +99,7 @@ def _find_crop_start_end(coord_ctr, crop_size, im_dim):
 
 
 def crop_image_around_centerline(im_in, ctr_in, im_out, crop_size, x_dim_half, y_dim_half):
-    im_in, im_ctr = Image(im_in), Image(ctr_in)
+    im_in, data_ctr = Image(im_in), Image(ctr_in).data
 
     im_new = im_in.copy()
     im_new.dim = tuple([crop_size, crop_size, im_in.dim[2]] + list(im_in.dim[3:]))
@@ -108,7 +108,7 @@ def crop_image_around_centerline(im_in, ctr_in, im_out, crop_size, x_dim_half, y
 
     x_lst, y_lst = [], []
     for zz in range(im_in.dim[2]):
-        x_ctr, y_ctr = center_of_mass(im_ctr.data[:, :, zz])
+        x_ctr, y_ctr = center_of_mass(np.array(data_ctr[:, :, zz]))
 
         x_start, x_end = _find_crop_start_end(x_ctr, crop_size, im_in.dim[0])
         y_start, y_end = _find_crop_start_end(y_ctr, crop_size, im_in.dim[1])
@@ -128,7 +128,7 @@ def crop_image_around_centerline(im_in, ctr_in, im_out, crop_size, x_dim_half, y
 
     im_new.save()
 
-    del im_in, im_ctr
+    del im_in
     del im_new
 
     return x_lst, y_lst

scripts/sct_image.py

@@ -559,8 +559,17 @@ def multicomponent_merge(fname_list):
     return im_out
 
 
-def orientation(im, ori=None, set=False, get=False, set_data=False, verbose=1, fname_out=''):
+def orientation(im, ori=None, set=False, get=False, set_data=False, verbose=1, fname_out=None):
+    """
+    :param fname_out: when set is True, where to save the output file
+                      (default: in cwd, named basename_orientation.ext)
+    :returns: when get, the orientation; when set, the changed image data (not saved)
+    """
     verbose = 0 if get else verbose
+
+    if fname_out is None:
+        fname_out = "{}_{}{}".format(im.file_name, ori, im.ext)
+
     printv('Get dimensions of data...', verbose)
     nx, ny, nz, nt, px, py, pz, pt = get_dimension(im)
 
@@ -580,9 +589,19 @@ def orientation(im, ori=None, set=False, get=False, set_data=False, verbose=1, f
         elif set:
             # set orientation
             printv('Change orientation...', verbose)
+            tmp_folder = tmp_create(verbose)
+            curdir = os.getcwd()
+            os.chdir(tmp_folder)
             im_out = set_orientation(im, ori)
+            os.chdir(curdir)
+            sct.rmtree(tmp_folder)
         elif set_data:
+            tmp_folder = tmp_create(verbose)
+            curdir = os.getcwd()
+            os.chdir(tmp_folder)
             im_out = set_orientation(im, ori, True)
+            os.chdir(curdir)
+            sct.rmtree(tmp_folder)
         else:
             im_out = None
 
@@ -646,12 +665,9 @@ def orientation(im, ori=None, set=False, get=False, set_data=False, verbose=1, f
         os.chdir(curdir)
         sct.rmtree(tmp_folder)
 
-    if fname_out:
+    if im_out is not None:
         im_out.setFileName(fname_out)
-        if fname_out != im.file_name + '_' + ori + im.ext:
-            sct.rm(im.file_name + '_' + ori + im.ext)
-    else:
-        im_out.setFileName(im.file_name + '_' + ori + im.ext)
+
     return im_out
 
 

scripts/sct_label_vertebrae.py

@@ -111,6 +111,10 @@ def get_parser():
                       type_value='file',
                       description='Initialize labeling by providing a text file which includes either -initz or -initcenter flag.',
                       mandatory=False)
+    parser.add_option(name="-initlabel",
+                      type_value='file',
+                      description='Initialize vertebral labeling by providing a nifti file that has a single disc label. An example of such file is a single voxel with value "3", which would be located at the posterior tip of C2-C3 disc. Such label file can be created using: sct_label_utils -i IMAGE_REF -create-viewer 3',
+                      mandatory=False)
     parser.add_option(name="-ofolder",
                       type_value="folder_creation",
                       description="Output folder.",
@@ -175,6 +179,9 @@ def main(args=None):
     initz = ''
     initcenter = ''
     initc2 = 'auto'
+    fname_initlabel = ''
+    fname_labelz = 'labelz.nii.gz'
+    initauto = False
     param = Param()
 
     # check user arguments
@@ -213,6 +220,9 @@ def main(args=None):
                 initz = [int(x) for x in arg_initfile[idx_arg + 1].split(',')]
             if arg == '-initcenter':
                 initcenter = int(arg_initfile[idx_arg + 1])
+    if '-initlabel' in arguments:
+        # get absolute path of label
+        fname_initlabel = os.path.abspath(arguments['-initlabel'])
     if '-initc2' in arguments:
         initc2 = 'manual'
     if '-param' in arguments:
@@ -235,19 +245,26 @@ def main(args=None):
 
     # create label to identify disc
     sct.printv('\nCreate label to identify disc...', verbose)
-    initauto = False
     if initz:
-        create_label_z('segmentation.nii.gz', initz[0], initz[1])  # create label located at z_center
+        create_label_z('segmentation.nii.gz', initz[0], initz[1], fname_labelz=fname_labelz)  # create label located at z_center
     elif initcenter:
         # find z centered in FOV
         nii = Image('segmentation.nii.gz')
         nii.change_orientation('RPI')  # reorient to RPI
         nx, ny, nz, nt, px, py, pz, pt = nii.dim  # Get dimensions
         z_center = int(round(nz / 2))  # get z_center
-        create_label_z('segmentation.nii.gz', z_center, initcenter)  # create label located at z_center
+        create_label_z('segmentation.nii.gz', z_center, initcenter, fname_labelz=fname_labelz)  # create label located at z_center
+    elif fname_initlabel:
+        import sct_label_utils
+        # subtract "1" to label value because due to legacy, in this code the disc C2-C3 has value "2", whereas in the
+        # recent version of SCT it is defined as "3". Therefore, when asking the user to define a label, we point to the
+        # new definition of labels (i.e., C2-C3 = 3).
+        sct_label_utils.main(['-i', fname_initlabel, '-add', '-1', '-o', fname_labelz])
+        # dilate label so that it is not lost when applying warping
+        import sct_maths
+        sct_maths.main(['-i', fname_labelz, '-dilate', '3', '-o', fname_labelz])
     else:
         initauto = True
-        # printv('\nERROR: You need to initialize the disc detection algorithm using one of these two options: -initz, -initcenter\n', 1, 'error')
 
     # Straighten spinal cord
     sct.printv('\nStraighten spinal cord...', verbose)
@@ -269,8 +286,6 @@ def main(args=None):
     # resample to 0.5mm isotropic to match template resolution
     sct.printv('\nResample to 0.5mm isotropic...', verbose)
     sct.run(['sct_resample', '-i', 'data_straight.nii', '-mm', '0.5x0.5x0.5', '-x', 'linear', '-o', 'data_straightr.nii'], verbose=verbose)
-    # sct.run('sct_resample -i segmentation.nii.gz -mm 0.5x0.5x0.5 -x linear -o segmentationr.nii.gz', verbose)
-    # sct.run('sct_resample -i labelz.nii.gz -mm 0.5x0.5x0.5 -x linear -o labelzr.nii', verbose)
 
     # Apply straightening to segmentation
     # N.B. Output is RPI
@@ -283,7 +298,7 @@ def main(args=None):
         init_disc = []
     else:
         # Apply straightening to z-label
-        sct.printv('\nDilate z-label and apply straightening...', verbose)
+        sct.printv('\nAnd apply straightening to label...', verbose)
         sct.run(['sct_apply_transfo', '-i', 'labelz.nii.gz', '-d', 'data_straightr.nii', '-w', 'warp_curve2straight.nii.gz', '-o', 'labelz_straight.nii.gz', '-x', 'nn'], verbose)
         # get z value and disk value to initialize labeling
         sct.printv('\nGet z and disc values from straight label...', verbose)
@@ -411,38 +426,12 @@ def vertebral_detection(fname, fname_seg, contrast, param, init_disc, verbose=1,
     :return:
     """
     sct.printv('\nLook for template...', verbose)
-    # if path_template == '':
-    #     # get path of SCT
-    #     from os import path
-    #     path_script = path.dirname(__file__)
-    #     path_sct = (path.dirname(path_script), 1)
-    #     folder_template = 'data/template/'
-    #     path_template = path_sct+folder_template
     sct.printv('Path template: ' + path_template, verbose)
 
     # adjust file names if MNI-Poly-AMU template is used
     fname_level = get_file_label(os.path.join(path_template, 'template'), 'vertebral', output='filewithpath')
     fname_template = get_file_label(os.path.join(path_template, 'template'), contrast.upper() + '-weighted', output='filewithpath')
 
-    # if not len(glob.glob(os.path.join(path_template, 'MNI-Poly-AMU*.*'))) == 0:
-    #     contrast = contrast.upper()
-    #     file_level = '*_level.nii.gz'
-    # else:
-    #     file_level = '*_levels.nii.gz'
-    #
-    # # retrieve file_template based on contrast
-    # try:
-    #     fname_template_list = glob.glob(os.path.join(path_template, '*' + contrast + '.nii.gz'))
-    #     fname_template = fname_template_list[0]
-    # except IndexError:
-    #     sct.printv('\nERROR: No template found. Please check the provided path.', 1, 'error')
-    # retrieve disc level from template
-    # try:
-    #     fname_level_list = glob.glob(os.path.join(path_template, file_level))
-    #     fname_level = fname_level_list[0]
-    # except IndexError:
-    #     sct.printv('\nERROR: File *_levels.nii.gz not found.', 1, 'error')
-
     # Open template and vertebral levels
     sct.printv('\nOpen template and vertebral levels...', verbose)
     data_template = Image(fname_template).data
@@ -660,14 +649,14 @@ def vertebral_detection(fname, fname_seg, contrast, param, init_disc, verbose=1,
 
 # Create label
 # ==========================================================================================
-def create_label_z(fname_seg, z, value):
+def create_label_z(fname_seg, z, value, fname_labelz='labelz.nii.gz'):
     """
     Create a label at coordinates x_center, y_center, z
     :param fname_seg: segmentation
     :param z: int
-    :return: fname_label
+    :param fname_labelz: string file name of output label
+    :return: fname_labelz
     """
-    fname_label = 'labelz.nii.gz'
     nii = Image(fname_seg)
     orientation_origin = nii.change_orientation('RPI')  # change orientation to RPI
     nx, ny, nz, nt, px, py, pz, pt = nii.dim  # Get dimensions
@@ -679,18 +668,18 @@ def create_label_z(fname_seg, z, value):
     # dilate label to prevent it from disappearing due to nearestneighbor interpolation
     from sct_maths import dilate
     nii.data = dilate(nii.data, [3])
-    nii.setFileName(fname_label)
+    nii.setFileName(fname_labelz)
     nii.change_orientation(orientation_origin)  # put back in original orientation
     nii.save()
-    return fname_label
+    return fname_labelz
 
 
 # Get z and label value
 # ==========================================================================================
 def get_z_and_disc_values_from_label(fname_label):
     """
-    Find z-value and label-value based on labeled image
-    :param fname_label: image that contains label
+    Find z-value and label-value based on labeled image in RPI orientation
+    :param fname_label: image in RPI orientation that contains label
     :return: [z_label, value_label] int list
     """
     nii = Image(fname_label)

scripts/sct_register_to_template.py

@@ -140,7 +140,7 @@ def get_parser():
                       type_value="multiple_choice",
                       description="""Remove temporary files.""",
                       mandatory=False,
-                      default_value='1',
+                      default_value='0',
                       example=['0', '1'])
     parser.add_option(name="-v",
                       type_value="multiple_choice",

scripts/sct_utils.py

@@ -319,8 +319,8 @@ def display_viewer_syntax(files, colormaps=[], minmax=[], opacities=[], mode='',
     sct.display_viewer_syntax([file1, file2], colormaps=['gray', 'red'], minmax=['', '0,1'], opacities=['', '0.7'])
     """
     list_viewer = ['fsleyes', 'fslview_deprecated', 'fslview']  # list of known viewers. Can add more.
-    dict_fslview = {'gray': 'Greyscale', 'red-yellow': 'Red-Yellow', 'blue-lightblue': 'Blue-Lightblue', 'red': 'Red', 'random': 'Random-Rainbow'}
-    dict_fsleyes = {'gray': 'greyscale', 'red-yellow': 'red-yellow', 'blue-lightblue': 'blue-lightblue', 'red': 'red', 'random': 'random'}
+    dict_fslview = {'gray': 'Greyscale', 'red-yellow': 'Red-Yellow', 'blue-lightblue': 'Blue-Lightblue', 'red': 'Red', 'random': 'Random-Rainbow', 'hsv': 'hsv'}
+    dict_fsleyes = {'gray': 'greyscale', 'red-yellow': 'red-yellow', 'blue-lightblue': 'blue-lightblue', 'red': 'red', 'random': 'random', 'hsv': 'hsv'}
     selected_viewer = None
 
     # find viewer

spinalcordtoolbox/gui/sagittal.py

@@ -92,8 +92,8 @@ def launch_sagittal_dialog(input_file, output_file, params):
     if not params.vertebraes:
         params.vertebraes = [3, 5]
     params.input_file_name = input_file.absolutepath
-    params.subtitle = u'Use Left/Right arrows to navigate the right-left direction' \
-                      '\nUse right click with left/right for brightness and up/down for contrast'
+    params.subtitle += u'Left/Right arrows: Navigate across slices.' \
+                       '\nRight click: Change brightness (left/right) and contrast (up/down).'
     controller = SagittalController(input_file, params, output_file)
     controller.reformat_image()