bump verison, merge pull request #17 from AMYPAD/dcm2nii

README.rst

@@ -9,13 +9,15 @@ Amyloid imaging to prevent Alzheimer's Disease.
 Install
 -------
 
-Choose one of the following:
+Requires Python 3.6 or greater. Choose one of the following:
 
 .. code:: sh
 
-    pip install amypet  # command line interface (CLI) version
+    pip install amypet       # command line interface (CLI) version
     pip install amypet[gui]  # CLI and graphical user interface (GUI) version
 
+For certain functionality (image trimming & resampling, DICOM to NIfTI converters) it may be required to also `pip install nimpa`.
+
 
 Usage
 -----

amypet/dcm2nii.py

@@ -0,0 +1,27 @@
+"""Convert DICOM folder to a NIfTI file
+
+Usage:
+  dcm2nii [options] <dcmpth>
+
+Arguments:
+  <dcmpth>  : Input folder containing DICOM files [default: DirChooser]
+
+Options:
+  --fcomment COMMENT  : Prefix to add to outputs
+  --timestamp  : Whether to include a timestamp in the output filename
+"""
+import logging
+from pathlib import Path
+
+from niftypet import nimpa
+
+log = logging.getLogger(__name__)
+
+
+def run(dcmpth, fcomment="converted-from-DICOM_", timestamp=True):
+    dcmpth = Path(dcmpth)
+    assert dcmpth.is_dir()
+    log.info("convert")
+    res = nimpa.dcm2nii(dcmpth, fprefix=fcomment, timestamp=timestamp)
+    log.debug("output file:%s", res)
+    return res

amypet/gui.py

@@ -249,7 +249,7 @@ def main(args=None, gui_mode=True):
     import niftypad.api
     import niftypad.models
 
-    from amypet import centiloid, imscroll, imtrimup
+    from amypet import centiloid, dcm2nii, imscroll, imtrimup
 
     parser = fix_subparser(MyParser(prog=None if gui_mode else "amypet"), gui_mode=gui_mode)
     sub_kwargs = {}
@@ -273,6 +273,9 @@ def argparser(prog, description=None, epilog=None, formatter_class=None):
     Func(imscroll.run, imscroll.__doc__, version=niftypad.__version__,
          python_deps=["miutil[nii,plot]", "tqdm"], argparser=argparser)
 
+    Func(dcm2nii.run, dcm2nii.__doc__, version=niftypad.__version__, python_deps=["nimpa"],
+         argparser=argparser)
+
     Func(imtrimup.run, imtrimup.__doc__, version=niftypad.__version__, python_deps=["nimpa"],
          argparser=argparser)
 

tests/test_dcm2nii.py

@@ -0,0 +1,14 @@
+from pathlib import Path
+
+import pytest
+
+
+@pytest.mark.timeout(30 * 60) # 30m
+def test_dcm2nii(datain):
+    dcmpth = Path(datain['mumapDCM'])
+    assert not list(dcmpth.glob('test_dcm2nii_*.nii*'))
+    dcm2nii = pytest.importorskip("amypet.dcm2nii")
+    dcm2nii.run(datain['mumapDCM'], fcomment="test_dcm2nii_")
+    assert list(dcmpth.glob('test_dcm2nii_*.nii*'))
+    for f in dcmpth.glob('test_dcm2nii_*.nii*'):
+        f.unlink()