Add CSA results on QC report

scripts/sct_process_segmentation.py

@@ -26,6 +26,7 @@
 from spinalcordtoolbox.aggregate_slicewise import aggregate_per_slice_or_level, save_as_csv, func_wa, func_std, \
     _merge_dict
 from spinalcordtoolbox.utils import parse_num_list
+from spinalcordtoolbox.reports.qc import generate_qc
 
 
 # TODO: Move this class somewhere else
@@ -115,6 +116,18 @@ def get_parser():
                       mandatory=False,
                       example=['0', '1'],
                       default_value='1')
+    parser.add_option(name='-qc',
+                      type_value='folder_creation',
+                      description='The path where the quality control generated content will be saved',
+                      default_value=None)
+    parser.add_option(name='-qc-dataset',
+                      type_value='str',
+                      description='If provided, this string will be mentioned in the QC report as the dataset the process was run on',
+                      )
+    parser.add_option(name='-qc-subject',
+                      type_value='str',
+                      description='If provided, this string will be mentioned in the QC report as the subject the process was run on',
+                      )
     parser.add_option(name='-v',
                       type_value='multiple_choice',
                       description='1: display on, 0: display off (default)',
@@ -129,6 +142,43 @@ def get_parser():
     return parser
 
 
+def _make_figure(metric):
+    """
+    Make a graph showing CSA and angles per slice.
+    :param metric: Dictionary of metrics
+    :return: image object
+    """
+    import tempfile
+    from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
+    from matplotlib.figure import Figure
+
+    fname_img = tempfile.NamedTemporaryFile().name + '.png'
+    z, csa, angle_ap, angle_rl = [], [], [], []
+    for key, value in metric.items():
+        z.append(key[0])
+        csa.append(value['MEAN(area)'])
+        angle_ap.append(value['MEAN(angle_AP)'])
+        angle_rl.append(value['MEAN(angle_RL)'])
+    # Make figure
+    fig = Figure()
+    FigureCanvas(fig)
+    ax = fig.add_subplot(211)
+    ax.plot(z, csa, 'k')
+    ax.plot(z, csa, 'k.')
+    ax.grid(True)
+    ax.set_ylabel('CSA [$mm^2$]')
+    ax = fig.add_subplot(212)
+    ax.plot(z, angle_ap, 'b')
+    ax.plot(z, angle_ap, 'b.')
+    ax.plot(z, angle_rl, 'r')
+    ax.plot(z, angle_rl, 'r.')
+    ax.grid(True)
+    ax.set_xlabel('Slice (Inferior-Superior direction)')
+    ax.set_ylabel('Angle [$deg$]')
+    fig.savefig(fname_img)
+    return fname_img
+
+
 def main(args):
     parser = get_parser()
     arguments = parser.parse(args)
@@ -171,6 +221,9 @@ def main(args):
             angle_correction = True
         elif arguments['-angle-corr'] == '0':
             angle_correction = False
+    path_qc = arguments.get("-qc", None)
+    qc_dataset = arguments.get("-qc-dataset", None)
+    qc_subject = arguments.get("-qc-subject", None)
 
     verbose = int(arguments.get('-v'))
     sct.init_sct(log_level=verbose, update=True)  # Update log level
@@ -191,6 +244,12 @@ def main(args):
                                                         group_funcs=group_funcs)
     metrics_agg_merged = _merge_dict(metrics_agg)
     save_as_csv(metrics_agg_merged, file_out, fname_in=fname_segmentation, append=append)
+
+    # QC report (only show CSA for clarity)
+    if path_qc is not None:
+        generate_qc(fname_segmentation, args=args, path_qc=os.path.abspath(path_qc), dataset=qc_dataset,
+                    subject=qc_subject, path_img=_make_figure(metrics_agg_merged), process='sct_process_segmentation')
+
     sct.display_open(file_out)
 
 

spinalcordtoolbox/reports/qc.py

@@ -12,6 +12,7 @@
 import datetime
 import io
 from string import Template
+from shutil import copyfile
 
 warnings.filterwarnings("ignore")
 
@@ -28,6 +29,7 @@
 import sct_utils as sct
 from spinalcordtoolbox.image import Image
 import spinalcordtoolbox.reports.slice as qcslice
+from spinalcordtoolbox import __sct_dir__
 
 logger = logging.getLogger(__name__)
 
@@ -313,7 +315,7 @@ def _save(self, fig, img_path, format='png', bbox_inches='tight', pad_inches=0.0
 
 
 class Params(object):
-    """Parses and stores the variables that will included into the QC details
+    """Parses and stores the variables that will be included into the QC details
     """
     def __init__(self, input_file, command, args, orientation, dest_folder, dpi=300, dataset=None, subject=None):
         """
@@ -378,11 +380,7 @@ def __init__(self, qc_params, usage):
         self.slice_name = qc_params.orientation
         self.qc_params = qc_params
         self.usage = usage
-
-        import spinalcordtoolbox
-        pardir = os.path.dirname(os.path.dirname(spinalcordtoolbox.__file__))
-        self.assets_folder = os.path.join(pardir, 'assets')
-
+        self.assets_folder = os.path.join(__sct_dir__, 'assets')
         self.img_base_name = 'bkg_img'
         self.description_base_name = "qc_results"
 
@@ -454,7 +452,7 @@ def _update_html_assets(self, json_data):
                              dest_full_path)
 
 
-def add_entry(src, process, args, path_qc, plane, background=None, foreground=None,
+def add_entry(src, process, args, path_qc, plane, path_img=None, path_img_overlay=None,
               qcslice=None,
               qcslice_operations=[],
               qcslice_layout=None,
@@ -470,8 +468,8 @@ def add_entry(src, process, args, path_qc, plane, background=None, foreground=No
     :param args:
     :param path_qc:
     :param plane:
-    :param background:
-    :param foreground:
+    :param path_img: Path to image to display
+    :param path_img_overlay: Path to image to display on top of path_img (will flip between the two)
     :param qcslice: spinalcordtoolbox.reports.slice:Axial
     :param qcslice_operations:
     :param qcslice_layout:
@@ -491,20 +489,18 @@ def layout(qslice):
             return qcslice_layout(qslice)
 
         layout(qcslice)
-    else:
+    elif path_img is not None:
         report.make_content_path()
-
-        def normalized(img):
-            return np.uint8(skimage.exposure.rescale_intensity(img, out_range=np.uint8))
-
-        skimage.io.imsave(qc_param.abs_overlay_img_path(), normalized(foreground))
-
-        if background is None:
-            qc_param.bkg_img_path = qc_param.overlay_img_path
+        report.update_description_file(skimage.io.imread(path_img).shape[:2])
+        copyfile(path_img, qc_param.abs_bkg_img_path())
+        if path_img_overlay is not None:
+            # User specified a second image to overlay
+            copyfile(path_img_overlay, qc_param.abs_overlay_img_path())
         else:
-            skimage.io.imsave(qc_param.abs_bkg_img_path(), normalized(background))
-
-        report.update_description_file(foreground.shape[:2])
+            # Copy the image both as "overlay" and "path_img_overlay", so it appears static.
+            # TODO: Leave the possibility in the reports/assets/js files to have static images (instead of having to
+            #  flip between two images).
+            copyfile(path_img, qc_param.abs_overlay_img_path())
 
     sct.printv('Successfully generated the QC results in %s' % qc_param.qc_results)
     sct.printv('Use the following command to see the results in a browser:')
@@ -521,7 +517,7 @@ def normalized(img):
 
 
 def generate_qc(fname_in1, fname_in2=None, fname_seg=None, args=None, path_qc=None, dataset=None, subject=None,
-                process=None):
+                path_img=None, process=None):
     """
     Generate a QC entry allowing to quickly review results. This function is the entry point and is called by SCT
     scripts (e.g. sct_propseg).
@@ -533,11 +529,16 @@ def generate_qc(fname_in1, fname_in2=None, fname_seg=None, args=None, path_qc=No
     :param path_qc: str: Path to save QC report
     :param dataset: str: Dataset name
     :param subject: str: Subject name
+    :param path_img: dict: Path to image to display (e.g., a graph), instead of computing the image from MRI.
     :param process: str: Name of SCT function. e.g., sct_propseg
     :return: None
     """
     logger.info('\n*** Generate Quality Control (QC) html report ***')
     dpi = 300
+    plane = None
+    qcslice_type = None
+    qcslice_operations = None
+    qcslice_layout = None
     # Get QC specifics based on SCT process
     # Axial orientation, switch between two input images
     if process in ['sct_register_multimodal', 'sct_register_to_template']:
@@ -570,6 +571,9 @@ def generate_qc(fname_in1, fname_in2=None, fname_seg=None, args=None, path_qc=No
         qcslice_type = qcslice.Sagittal([Image(fname_in1), Image(fname_seg)], p_resample=None)
         qcslice_operations = [QcImage.highlight_pmj]
         qcslice_layout = lambda x: x.single()
+    # Metric outputs (only graphs)
+    elif process in ['sct_process_segmentation']:
+        assert os.path.isfile(path_img)
     else:
         raise ValueError("Unrecognized process: {}".format(process))
 
@@ -581,6 +585,7 @@ def generate_qc(fname_in1, fname_in2=None, fname_seg=None, args=None, path_qc=No
         dataset=dataset,
         subject=subject,
         plane=plane,
+        path_img=path_img,
         dpi=dpi,
         qcslice=qcslice_type,
         qcslice_operations=qcslice_operations,