Merge pull request #1272 from EmmaRenauld/fix_issue1122

Nicer print_info. Now ~ the same for all data types!

Author: arnaudbore

src/scilpy/cli/scil_header_print_info.py

@@ -1,15 +1,19 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
-Print the raw header from the provided file or only the specified keys.
-Support trk, nii and mgz files.
+Prints the raw header from the provided file or only the specified keys.
+Supports trk, nii and mgz files.
+
+By default, a simple summary view is shown. Use --all for a more complete
+display.
 """
 
 import argparse
 import logging
 import pprint
 
 import nibabel as nib
+from nibabel import aff2axcodes
 
 from scilpy.io.utils import assert_inputs_exist, add_verbose_arg
 from scilpy.utils.filenames import split_name_with_nii
@@ -23,10 +27,11 @@ def _build_arg_parser():
 
     p.add_argument('in_file',
                    help='Input file (trk, nii and mgz).')
-    p.add_argument('--keys', nargs='+',
-                   help='Print only the specified keys.')
-    p.add_argument('--print_affine', action='store_true',
-                   help="Print nibabel's affine.")
+    g = p.add_mutually_exclusive_group()
+    g.add_argument('--raw_header', action='store_true',
+                   help="Print the whole header as received by nibabel.")
+    g.add_argument('--keys', nargs='+',
+                   help="Print only the specified keys from nibabel's header")
 
     add_verbose_arg(p)
 
@@ -55,16 +60,44 @@ def main():
                 parser.error('Key {} is not in the header of {}.'.format(key,
                              args.in_file))
             print(" '{}': {}".format(key, header[key]))
-    else:
+    elif args.raw_header:
         pp = pprint.PrettyPrinter(indent=1)
         pp.pprint(header)
-
-    if args.print_affine:
-        if in_extension in ['.tck', '.trk']:
+    else:
+        # mrinfo-type of print.
+
+        # Getting info:
+        if in_extension in ['.nii', '.nii.gz', '.mgz']:
+            img = nib.load(args.in_file)  # Data type and affine require img
+            affine = img.affine
+            dtype = img.get_data_dtype().type
+            if in_extension in ['.nii', '.nii.gz']:
+                nb_dims = header['dim'][0]
+                dims = header['dim'][1:1 + nb_dims]
+                vox_size = header['dim'][5:5 + nb_dims]
+            elif in_extension == '.mgz':
+                dims = header['dims']
+                vox_size = header['delta']
+        else:
             affine = nib.streamlines.load(args.in_file, lazy_load=True).affine
-        else:  # in_extension in ['.nii', '.nii.gz', '.mgz']:
-            affine = nib.load(args.in_file).affine
-        print(" '{}': {}".format('affine', affine))
+
+            # 'dimensions' and 'voxel_sizes' exist for both tck and trk
+            dims = header['dimensions']
+            vox_size = header['voxel_sizes']
+
+            if in_extension == '.trk':
+                dtype = 'float32' # always float32 for trk
+            else:
+                dtype = header['datatype']
+
+        print("**************************************")
+        print("File name:    {}".format(args.in_file))
+        print("**************************************")
+        print("  Dimensions: {}".format(dims))
+        print("  Voxel size: {}".format(vox_size))
+        print("  Datatype: {}".format(dtype))
+        print("  Orientation: {}".format(aff2axcodes(affine)))
+        print("  Afine (vox2rasmm):\n{}".format(affine))
 
 
 if __name__ == "__main__":

src/scilpy/cli/tests/test_header_print_info.py

@@ -24,6 +24,21 @@ def test_execution_img(script_runner, monkeypatch):
     assert ret.success
 
 
+def test_execution_img_keys(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_img = os.path.join(SCILPY_HOME, 'others', 'fa.nii.gz')
+    ret = script_runner.run(['scil_header_print_info', in_img,
+                             '--keys', 'pixdim'])
+    assert ret.success
+
+
+def test_execution_img_raw(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_img = os.path.join(SCILPY_HOME, 'others', 'fa.nii.gz')
+    ret = script_runner.run(['scil_header_print_info', in_img,
+                             '--raw_header'])
+    assert ret.success
+
 def test_execution_tractogram(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
     in_tracto = os.path.join(SCILPY_HOME, 'others', 'IFGWM.trk')