add annotation Module

AnnotationModule.py

@@ -0,0 +1,102 @@
+import logging
+from BaseImage import printMaskHelper
+from skimage import io, img_as_ubyte
+from skimage.draw import polygon
+import os
+from pathlib import PurePosixPath
+
+import xml.etree.ElementTree as ET
+import numpy as np
+
+""" 
+xmlMask will create a mask that is true inside the annotated region described in the specified xml file. The xml file must follow the ImageScope format, the minimal components of which are:
+
+<?xml version="1.0" encoding="UTF-8"?>
+<Annotations>
+<Annotation>
+<Regions>
+<Region>
+<Vertices>
+<Vertex X="56657.4765625" Y="78147.3984375"/>
+<Vertex X="56657.4765625" Y="78147.3984375"/>
+<Vertex X="56664.46875" Y="78147.3984375"/>
+</Region>
+</Regions>
+</Annotation>
+</Annotations>
+
+With more <Annotation> or <Region> blocks as needed for additional annotations. There is no functional difference between multiple <Annotation> blocks and one <Annotation> blocks with multiple <Region> blocks
+"""
+
+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([(int(float(vertex.get('X'))),int(float(vertex.get('Y')))) for vertex in vertices.findall('Vertex')])
+
+    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:
+        poly = np.asarray(pointSet)
+        rr, cc = polygon(poly[:,1],poly[:,0],mask.shape)
+        mask[rr,cc] = 1
+
+    return mask
+
+def xmlMask(s,params):
+    logging.info(f"{s['filename']} - \txmlMask")
+    mask = s["img_mask_use"]
+
+    xml_basepath = params.get("xml_filepath",None)
+    xml_suffix = params.get("xml_suffix", "")
+    if not xml_basepath:
+        xml_basepath = s["dir"]
+
+    xml_fname = xml_basepath + os.sep + PurePosixPath(s['filename']).stem + 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