Update FRAP scripts to use roi_service.getShapeStatsRestricted()

practical/python/server/simple_frap.py

@@ -20,7 +20,7 @@
 # ------------------------------------------------------------------------------
 
 """
-Simple FRAP plots from Rectangles on images.
+Simple FRAP plots from Ellipses on images.
 This an OMERO script that runs server-side.
 """
 
@@ -40,7 +40,7 @@
 
 def run(conn, params):
     """
-    For each image, getTiles() for FRAP rectangle and plot mean intensity.
+    For each image, getTiles() for FRAP Ellipse and plot mean intensity.
 
     Returns list of images
     @param conn   The BlitzGateway connection
@@ -66,32 +66,28 @@ def run(conn, params):
     for image in images:
         print "---- Processing image", image.id
         result = roi_service.findByImage(image.getId(), None)
-        x = 0
-        y = 0
-        width = 0
-        height = 0
+
+        # Simply use any Ellipse we find...
+        shape_id = None
         for roi in result.rois:
             print "ROI:  ID:", roi.getId().getValue()
             for s in roi.copyShapes():
-                if type(s) == omero.model.RectangleI:
-                    x = s.getX().getValue()
-                    y = s.getY().getValue()
-                    width = s.getWidth().getValue()
-                    height = s.getHeight().getValue()
-        print "Rectangle:", x, y, width, height
-        if x == 0:
-            print "  No Rectangle found for this image"
+                if type(s) == omero.model.EllipseI:
+                    shape_id = s.id.val
+        print "Shape:", shape_id
+        if shape_id is None:
+            print "  No Ellipse found for this image"
             continue
 
-        c, z = 0, 0
-        tile = (int(x), int(y), int(width), int(height))
-        pixels = image.getPrimaryPixels()
+        # Get pixel intensities for first Channel
+        the_c = 0
+        the_z = 0
         size_t = image.getSizeT()
-        zct_list = [(z, c, t, tile) for t in range(size_t)]
-        planes = pixels.getTiles(zct_list)
         meanvalues = []
-        for i, p in enumerate(planes):
-            meanvalues.append(p.mean())
+        for t in range(size_t):
+            stats = roi_service.getShapeStatsRestricted([shape_id],
+                                                        the_z, t, [the_c])
+            meanvalues.append(stats[0].mean[the_c])
 
         print meanvalues
 
@@ -110,13 +106,12 @@ def run(conn, params):
             plt.subplot(111)
             plt.plot(meanvalues)
             fig.canvas.draw()
-            data = np.fromstring(fig.canvas.tostring_rgb(),
-                                 dtype=np.uint8, sep='')
-            data = data.reshape(fig.canvas.get_width_height()[::-1] + (3,))
-
-            red = data[::, ::, 0]
-            green = data[::, ::, 1]
-            blue = data[::, ::, 2]
+            fig.savefig('plot.png')
+            pil_img = Image.open('plot.png')
+            np_array = np.asarray(pil_img)
+            red = np_array[::, ::, 0]
+            green = np_array[::, ::, 1]
+            blue = np_array[::, ::, 2]
             plane_gen = iter([red, green, blue])
             plot_name = image.getName() + "_FRAP_plot"
             i = conn.createImageFromNumpySeq(plane_gen, plot_name, sizeC=3,
@@ -134,7 +129,7 @@ def run(conn, params):
     client = scripts.client(
         'Scipy_Gaussian_Filter.py',
         """
-    This script does simple FRAP analysis using Rectangle ROIs previously
+    This script does simple FRAP analysis using Ellipse ROIs previously
     saved on images. If matplotlib is installed, data is plotted and new
     OMERO images are created from the plots.
         """,

practical/python/server/simple_frap_with_figure.py

@@ -20,7 +20,7 @@
 # ------------------------------------------------------------------------------
 
 """
-Simple FRAP plots from Rectangles on images and creates an OMERO.figure.
+Simple FRAP plots from Ellipses on images and creates an OMERO.figure.
 
 This an OMERO script that runs server-side.
 """
@@ -227,7 +227,7 @@ def create_omero_figure(conn, images, plots):
 
 def run(conn, params):
     """
-    For each image, getTiles() for FRAP rectangle and plot mean intensity.
+    For each image, getTiles() for FRAP Ellipse and plot mean intensity.
 
     Returns list of images
     @param conn   The BlitzGateway connection
@@ -253,32 +253,28 @@ def run(conn, params):
     for image in images:
         print "---- Processing image", image.id
         result = roi_service.findByImage(image.getId(), None)
-        x = 0
-        y = 0
-        width = 0
-        height = 0
+
+        # Simply use any Ellipse we find...
+        shape_id = None
         for roi in result.rois:
             print "ROI:  ID:", roi.getId().getValue()
             for s in roi.copyShapes():
-                if type(s) == omero.model.RectangleI:
-                    x = s.getX().getValue()
-                    y = s.getY().getValue()
-                    width = s.getWidth().getValue()
-                    height = s.getHeight().getValue()
-        print "Rectangle:", x, y, width, height
-        if x == 0:
-            print "  No Rectangle found for this image"
+                if type(s) == omero.model.EllipseI:
+                    shape_id = s.id.val
+        print "Shape:", shape_id
+        if shape_id is None:
+            print "  No Ellipse found for this image"
             continue
 
-        c, z = 0, 0
-        tile = (int(x), int(y), int(width), int(height))
-        pixels = image.getPrimaryPixels()
+        # Get pixel intensities for first Channel
+        the_c = 0
+        the_z = 0
         size_t = image.getSizeT()
-        zct_list = [(z, c, t, tile) for t in range(size_t)]
-        planes = pixels.getTiles(zct_list)
         meanvalues = []
-        for i, p in enumerate(planes):
-            meanvalues.append(p.mean())
+        for t in range(size_t):
+            stats = roi_service.getShapeStatsRestricted([shape_id],
+                                                        the_z, t, [the_c])
+            meanvalues.append(stats[0].mean[the_c])
 
         print meanvalues
 
@@ -317,7 +313,7 @@ def run(conn, params):
     client = scripts.client(
         'Simple_FRAP.py',
         """
-    This script does simple FRAP analysis using Rectangle ROIs previously
+    This script does simple FRAP analysis using Ellipse ROIs previously
     saved on images. If matplotlib is installed, data is plotted and new
     OMERO images are created from the plots.
         """,