add annotation Module

AnnotationModule.py

@@ -0,0 +1,81 @@
+import logging
+from BaseImage import printMaskHelper
+from skimage import io, img_as_ubyte
+import os
+
+import xml.etree.ElementTree as ET
+import numpy as np
+import cv2
+
+def get_points(xml_fname):
+    """Parses the xml file to get those annotations as lists of verticies"""
+    # create element tree object
+    tree = ET.parse(xml_fname)
+
+    # get root element
+    root = tree.getroot()
+
+    points = []
+
+    for annotation in root.findall('Annotation'):
+        for regions in annotation.findall('Regions'):
+            for region in regions.findall('Region'):
+                for vertices in region.findall('Vertices'):
+                    points.append([None] * len(vertices.findall('Vertex')))
+                    for k, vertex in enumerate(vertices.findall('Vertex')):
+                        points[-1][k] = (int(float(vertex.get('X'))), int(float(vertex.get('Y'))))
+
+    return points
+
+
+def resize_points(points, resize_factor):
+    for k, pointSet in enumerate(points):
+        points[k] = [(int(p[0] * resize_factor), int(p[1] * resize_factor)) for p in pointSet]
+
+    return points.copy()
+
+def mask_out_annotation(s,xml_fname):
+    """Returns the mask of annotations"""
+
+    points = get_points(xml_fname)
+
+    resize_factor = np.shape(s["img_mask_use"])[1] / s["image_base_size"][0]
+
+    points = resize_points(points, resize_factor)
+
+    mask = np.zeros((np.shape(s["img_mask_use"])[0],np.shape(s["img_mask_use"])[1]),dtype=np.uint8)
+
+    for pointSet in points:
+        cv2.fillPoly(mask, [np.asarray(pointSet).reshape((-1, 1, 2))], 1)
+
+    return mask
+
+def xmlMask(s,params):
+    logging.info(f"{s['filename']} - \txmlMask")
+    mask = s["img_mask_use"]
+
+    xml_basepath = params.get("xml_filepath","")
+    xml_suffix = params.get("xml_suffix", "")
+    if len(xml_basepath)==0:
+        xml_basepath = s["dir"]
+
+    xml_fname = xml_basepath + os.sep + s['filename'][:s['filename'].rindex('.')] + xml_suffix + '.xml'
+
+    logging.info(f"{s['filename']} - \tusing {xml_fname}")
+
+    annotationMask = mask_out_annotation(s,xml_fname) > 0
+    io.imsave(s["outdir"] + os.sep + s["filename"] + "_xmlMask.png", img_as_ubyte(annotationMask))
+
+    prev_mask = s["img_mask_use"]
+    s["img_mask_use"] = prev_mask & annotationMask
+
+    s.addToPrintList("xmlMask",
+                     printMaskHelper(params.get("mask_statistics", s["mask_statistics"]), prev_mask, s["img_mask_use"]))
+
+    if len(s["img_mask_use"].nonzero()[0]) == 0:  # add warning in case the final tissue is empty
+        logging.warning(
+            f"{s['filename']} - After AnnotationModule.xmlMask NO tissue remains detectable! Downstream modules likely to be incorrect/fail")
+        s["warnings"].append(
+            f"After AnnotationModule.xmlMask NO tissue remains detectable! Downstream modules likely to be incorrect/fail")
+
+    return

BaseImage.py

@@ -58,8 +58,10 @@ def __init__(self, fname, fname_outdir, params):
         self["dir"] = os.path.dirname(fname)
 
         self["os_handle"] = openslide.OpenSlide(fname)
+        self["image_base_size"] = self["os_handle"].dimensions
         self["image_work_size"] = params.get("image_work_size", "1.25x")
         self["mask_statistics"] = params.get("mask_statistics", "relative2mask")
+        self["base_mag"] = getMag(self, params)
         self.addToPrintList("base_mag", getMag(self, params))
 
         mask_statistics_types = ["relative2mask", "absolute", "relative2image"]

config_example_AnnotationModule.ini

@@ -0,0 +1,33 @@
+[pipeline]
+steps= BasicModule.getBasicStats
+    AnnotationModule.xmlMask
+    SaveModule.saveFinalMask
+    SaveModule.saveThumbnails
+    BasicModule.finalComputations
+
+
+[BaseImage.BaseImage]
+image_work_size = 1.25x
+
+#three options: relative2mask, absolute, relative2image
+mask_statistics = relative2mask
+
+confirm_base_mag: False
+
+
+[BasicModule.getBasicStats]
+image_work_size = 1.25x
+
+
+[AnnotationModule.xmlMask]
+#leave blank to replacing image filename extension with "xml", as in: /path/to/file/base_filename_image.svs -> /path/to/file/base_filename_image.xml
+xml_filepath =
+#suffix is inserted before extension, as in: /path/to/file/base_filename_image.svs -> /path/to/file/base_filename_image{suffix}.xml
+xml_suffix =
+
+[SaveModule.saveFinalMask] 
+overlay: True 
+
+[SaveModule.saveThumbnails] 
+image_work_size: 1.25x 
+small_dim: 500