Add roiimport plugin and readers for idr0012 and idr0016

plugins/IDR0012Reader.py

@@ -0,0 +1,65 @@
+from ROIReader import ROIReader
+
+from math import isnan
+
+import omero
+from omero.rtypes import rint, rstring
+
+
+class IDR0012Reader(ROIReader):
+
+    # Relevant columns in the HDF5 file
+    COLUMN_X = "x"
+    COLUMN_Y = "y"
+    COLUMN_CLASS = "class"
+    COLUMN_FIELD = "spot"
+
+    cellClasses = {'AF': 'Actin fibre',
+                   'BC': 'Big cell',
+                   'C': 'Condensed cell',
+                   'D': 'Debris',
+                   'LA': 'Lamellipodia',
+                   'M': 'Metaphase',
+                   'MB': 'Membrane blebbing',
+                   'N': 'Normal cell',
+                   'P': 'Protrusion/Elongation',
+                   'Z': 'Telophase'}
+
+    def nextROIs(self):
+
+        for plate in self.h5f.iter_nodes(self.h5f.root):
+            for well in self.h5f.iter_nodes(plate):
+                rois = {}
+                for row in well.iterrows():
+                    x = row[self.COLUMN_X]
+                    y = row[self.COLUMN_Y]
+                    cl = row[self.COLUMN_CLASS]
+                    fld = row[self.COLUMN_FIELD]
+
+                    if not (isnan(x) or isnan(y)):
+                        roi = omero.model.RoiI()
+                        point = omero.model.PointI()
+                        point.x = x
+                        point.y = y
+                        point.theZ = rint(0)
+                        point.theT = rint(0)
+                        if cl:
+                            if cl in self.cellClasses:
+                                point.textValue = rstring(
+                                    self.cellClasses[cl])
+                            else:
+                                point.textValue = rstring(cl)
+
+                        roi.addShape(point)
+
+                        if fld not in rois:
+                            rois[fld] = []
+
+                        rois[fld].append(roi)
+
+                for fld in rois:
+                    wella = well._v_name[0]
+                    wellb = "%d" % int(well._v_name[1:])
+                    wellname = wella + wellb
+                    imgpos = '%s | %s | %s' % (plate._v_name, wellname, fld)
+                    yield imgpos, rois[fld]

plugins/IDR0016Reader.py

@@ -0,0 +1,118 @@
+from ROIReader import ROIReader
+
+import sys
+from math import isnan
+
+import omero
+from omero.rtypes import rint, rstring
+
+from tables import open_file
+
+
+class IDR0016Reader(ROIReader):
+
+    # Relevant columns in the HDF5 file
+    COLUMN_IMAGENUMBER = "ImageNumber"
+    COLUMN_WELLPOSITION = "Image_Metadata_CPD_WELL_POSITION"
+    COLUMN_PLATEID = "Image_Metadata_PlateID"
+    COLUMN_FIELD = "Image_Metadata_Site"
+
+    NUCLEI_LOCATION_X = "Nuclei_Location_Center_X"
+    NUCLEI_LOCATION_Y = "Nuclei_Location_Center_Y"
+    CELLS_LOCATION_X = "Cells_Location_Center_X"
+    CELLS_LOCATION_Y = "Cells_Location_Center_Y"
+    CYTOPLASM_LOCATION_X = "Cytoplasm_Location_Center_X"
+    CYTOPLASM_LOCATION_Y = "Cytoplasm_Location_Center_Y"
+
+    def __init__(self, hdfFile):
+        try:
+            h5f = open_file(hdfFile, "a")
+            objs = h5f.get_node("/Objects")
+            imgnoColumn = objs.colinstances[self.COLUMN_IMAGENUMBER]
+            if not imgnoColumn.is_indexed:
+                sys.stdout.write("Create index for the image number column...")
+                imgnoColumn.create_index()
+        except Exception:
+            sys.stderr.write("Could not create index. This will significantly "
+                             "slow down reading performance!")
+        finally:
+            h5f.close()
+
+        ROIReader.__init__(self, hdfFile)
+
+    def _mapImageNumberToPosition(self):
+        """
+        Maps the ImageNumber in the HDF5 file to plate positions
+        :param args: The arguments array
+        :return: A dictionary mapping the ImageNumber in the HDF5 file to
+                 plate positions (in form 'PlateName | Well | Field')
+        """
+        imgdict = {}
+        try:
+            imgs = self.h5f.get_node("/Images")
+
+            # Map image number to image position (in form
+            # 'PlateName | Well | Field')
+            for row in imgs:
+                well = row[self.COLUMN_WELLPOSITION]
+                # Wells can have leading zero, e.g. A03, have to strip the zero
+                # to match e.g. A3
+                wella = well[0]
+                wellb = "%d" % int(well[1:])
+                well = wella + wellb
+                imgpos = "%s | %s | %s" % (row[self.COLUMN_PLATEID], well,
+                                           row[self.COLUMN_FIELD])
+                imgdict[row[self.COLUMN_IMAGENUMBER]] = imgpos
+        except Exception:
+            sys.stderr.write("Could not map image numbers to plate positions.")
+        return imgdict
+
+    def nextROIs(self):
+        imgNumbers = self._mapImageNumberToPosition()
+
+        objs = self.h5f.get_node("/Objects")
+        for imgNumber in imgNumbers:
+            imgpos = imgNumbers[imgNumber]
+            rois = []
+            query = self.COLUMN_IMAGENUMBER + " == " + str(imgNumber)
+            for row in objs.where(query):
+                x = row[self.NUCLEI_LOCATION_X]
+                y = row[self.NUCLEI_LOCATION_Y]
+                if not (isnan(x) or isnan(y)):
+                    roi = omero.model.RoiI()
+                    point = omero.model.PointI()
+                    point.x = x
+                    point.y = y
+                    point.theZ = rint(0)
+                    point.theT = rint(0)
+                    point.textValue = rstring("Nucleus")
+                    roi.addShape(point)
+                    rois.append(roi)
+
+                x = row[self.CELLS_LOCATION_X]
+                y = row[self.CELLS_LOCATION_Y]
+                if not (isnan(x) or isnan(y)):
+                    roi = omero.model.RoiI()
+                    point = omero.model.PointI()
+                    point.x = x
+                    point.y = y
+                    point.theZ = rint(0)
+                    point.theT = rint(0)
+                    point.textValue = rstring("Cell")
+                    roi.addShape(point)
+                    rois.append(roi)
+
+                x = row[self.CYTOPLASM_LOCATION_X]
+                y = row[self.CYTOPLASM_LOCATION_Y]
+                if not (isnan(x) or isnan(y)):
+                    roi = omero.model.RoiI()
+                    point = omero.model.PointI()
+                    point.x = x
+                    point.y = y
+                    point.theZ = rint(0)
+                    point.theT = rint(0)
+                    point.textValue = rstring("Cytoplasm")
+                    roi.addShape(point)
+                    rois.append(roi)
+
+            yield imgpos, rois

plugins/ROIReader.py

@@ -0,0 +1,21 @@
+from tables import open_file
+
+
+class ROIReader:
+
+    def __init__(self, hdfFile):
+        self.h5f = open_file(hdfFile, "r")
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type, exc_value, traceback):
+        self.h5f.close()
+
+    def nextROIs(self):
+        """
+        Get the next batch of ROIs for an Image
+        :return: Image position in form 'PlateName | Well | Field'
+                 and a list of ROIs for this image
+        """
+        raise NotImplementedError("Not implemented yet")