Fixes and improvements (by mtnhuck)

.travis.yml

@@ -0,0 +1,22 @@
+language: python
+
+cache:
+  directories:
+    - $HOME/.cache/pip
+
+python:
+    - 2.7
+    - 3.5
+    - 3.6
+    - 3.7
+
+install:
+    - travis_retry pip install -e .
+    - travis_retry pip install pytest pytest-cov coverage
+
+script:
+    - python -m pytest --cov=bids2nda -s -v bids2nda
+
+after_success:
+    - travis_retry pip install codecov
+    - codecov

README.md

@@ -23,7 +23,7 @@ Extract NIHM Data Archive compatible metadata from Brain Imaging Data Structure
 
     optional arguments:
       -h, --help        show this help message and exit
-      
+
 
 ## GUID_MAPPING file format
 The is the file format produced by the GUID Tool: one line per subject in the format
@@ -32,3 +32,7 @@ The is the file format produced by the GUID Tool: one line per subject in the fo
 
 ## Example outputs
 See [/examples](/examples)
+
+## Notes:
+Column experiment_id must be manually filled in for now.
+This is based on experiment ID's received from NDA after setting the study up through the NDA website [here](https://ndar.nih.gov/user/dashboard/collections.html).

bids2nda/main.py

@@ -15,6 +15,7 @@
 import nibabel as nb
 import json
 import pandas as pd
+import numpy as np
 
 
 # Gather our code in a main() function
@@ -74,6 +75,55 @@ def dict_append(d, key, value):
         d[key] = [value, ]
 
 
+def cosine_to_orientation(iop):
+    """Deduce slicing from cosines
+
+    From http://nipy.org/nibabel/dicom/dicom_orientation.html#dicom-voxel-to
+    -patient-coordinate-system-mapping
+
+    From Section C.7.6.1.1.1 we see that the "positive row axis" is left to
+    right, and is the direction of the rows, given by the direction of last
+    pixel in the first row from the first pixel in that row. Similarly the
+    "positive column axis" is top to bottom and is the direction of the columns,
+    given by the direction of the last pixel in the first column from the first
+    pixel in that column.
+
+    Let's rephrase: the first three values of "Image Orientation Patient" are
+    the direction cosine for the "positive row axis". That is, they express the
+    direction change in (x, y, z), in the DICOM patient coordinate system
+    (DPCS), as you move along the row. That is, as you move from one column to
+    the next. That is, as the column array index changes. Similarly, the second
+    triplet of values of "Image Orientation Patient" (img_ornt_pat[3:] in
+    Python), are the direction cosine for the "positive column axis", and
+    express the direction you move, in the DPCS, as you move from row to row,
+    and therefore as the row index changes.
+
+    Parameters
+    ----------
+    iop: list of float
+       Values of the ImageOrientationPatient field
+
+    Returns
+    -------
+    {'Axial', 'Coronal', 'Sagittal'}
+    """
+    # Solution based on https://stackoverflow.com/a/45469577
+    iop_round = np.round(iop)
+    plane = np.cross(iop_round[0:3], iop_round[3:6])
+    plane = np.abs(plane)
+    if plane[0] == 1:
+        return "Sagittal"
+    elif plane[1] == 1:
+        return "Coronal"
+    elif plane[2] == 1:
+        return "Axial"
+    else:
+        raise RuntimeError(
+            "Could not deduce the image orientation of %r. 'plane' value is %r"
+            % (iop, plane)
+        )
+
+
 def run(args):
 
     guid_mapping = dict([line.split(" - ") for line in open(args.guid_mapping).read().split("\n") if line != ''])
@@ -155,18 +205,29 @@ def run(args):
         else:
             description = suffix
             dict_append(image03_dict, 'experiment_id', '')
+        # Shortcut for the global.const section -- apparently might not be flattened fully
+        metadata_const = metadata.get('global', {}).get('const', {})
         dict_append(image03_dict, 'image_description', description)
         dict_append(image03_dict, 'scan_type', suffix_to_scan_type[suffix])
         dict_append(image03_dict, 'scan_object', "Live")
         dict_append(image03_dict, 'image_file_format', "NIFTI")
         dict_append(image03_dict, 'image_modality', "MRI")
         dict_append(image03_dict, 'scanner_manufacturer_pd', metadata.get("Manufacturer", ""))
         dict_append(image03_dict, 'scanner_type_pd', metadata.get("ManufacturersModelName", ""))
-        dict_append(image03_dict, 'scanner_software_versions_pd', metadata.get("HardcopyDeviceSoftwareVersion", ""))
+        dict_append(image03_dict, 'scanner_software_versions_pd', metadata.get("SoftwareVersions", ""))
         dict_append(image03_dict, 'magnetic_field_strength', metadata.get("MagneticFieldStrength", ""))
         dict_append(image03_dict, 'mri_echo_time_pd', metadata.get("EchoTime", ""))
         dict_append(image03_dict, 'flip_angle', metadata.get("FlipAngle", ""))
         dict_append(image03_dict, 'receive_coil', metadata.get("ReceiveCoilName", ""))
+        # ImageOrientationPatientDICOM is populated by recent dcm2niix,
+        # and ImageOrientationPatient might be provided by exhastive metadata
+        # record done by heudiconv
+        iop = metadata.get(
+            'ImageOrientationPatientDICOM',
+            metadata_const.get("ImageOrientationPatient", None)
+        )
+        dict_append(image03_dict, 'image_orientation', cosine_to_orientation(iop) if iop else '')
+
         dict_append(image03_dict, 'transformation_performed', 'Yes')
         dict_append(image03_dict, 'transformation_type', 'BIDS2NDA')
 
@@ -194,6 +255,8 @@ def run(args):
         dict_append(image03_dict, 'image_resolution1', nii.header.get_zooms()[0])
         dict_append(image03_dict, 'image_resolution2', nii.header.get_zooms()[1])
         dict_append(image03_dict, 'image_resolution3', nii.header.get_zooms()[2])
+        dict_append(image03_dict, 'image_slice_thickness', metadata_const.get("SliceThickness", nii.header.get_zooms()[2]))
+        dict_append(image03_dict, 'photomet_interpret', metadata.get("global",{}).get("const",{}).get("PhotometricInterpretation",""))
         if len(nii.shape) > 3:
             image_resolution4 = nii.header.get_zooms()[3]
         else:

bids2nda/tests/test_helpers.py

@@ -0,0 +1,8 @@
+from ..main import cosine_to_orientation
+
+
+def test_cosine_to_orientation():
+    assert cosine_to_orientation([0.9, -0.03, -0.1, 0.03, 0.9, 0.1]) == 'Axial'
+    assert cosine_to_orientation([0, 0.9, 0.1, 0.03, 0.1, -0.9]) == 'Sagittal'
+
+

setup.py

@@ -43,7 +43,9 @@
 
     # You can just specify the packages manually here if your project is
     # simple. Or you can use find_packages.
-    packages=["bids2nda"],
+    packages=["bids2nda",
+              "bids2nda.tests",
+              ],
 
     # List run-time dependencies here.  These will be installed by pip when your
     # project is installed.