Add multi render.

test/convert_to_vtk.py

@@ -0,0 +1,31 @@
+import pickle
+import vtk
+import os
+from stack3d.study.components import StudyData, MouseData, TimepointData
+import stack3d.formats.unet
+
+
+def skeleton_to_vtp(work_dir, study_collection):
+
+    for eachStudy in study_collection:
+        print "Converting Study: ", eachStudy.raw_data_path
+        study_dir = work_dir + "/" + eachStudy.raw_data_path
+        for eachMouse in eachStudy.mice:
+            print "Converting Mouse: ", eachMouse.raw_data_path
+            mouse_dir = study_dir + "/" + eachMouse.raw_data_path
+            for eachTimePoint in eachMouse.timepoints:
+                print "Converting Time: ", eachTimePoint.raw_data_path
+                time_dir = mouse_dir + "/" + eachTimePoint.raw_data_path
+                base_path = "/analysis_analysis/skeleton.pkl"
+                if os.path.isfile(time_dir + base_path):
+                    output_path = os.path.dirname(os.path.realpath(time_dir + "/analysis_analysis/skeleton.vtp"))
+                    polydata = stack3d.formats.unet.skeleton_to_vtp(time_dir + base_path)
+                    writer = vtk.vtkXMLPolyDataWriter()
+                    writer.SetInputData(polydata)
+                    writer.SetFileName(output_path + "/skeleton.vtp")
+                    writer.Write()
+
+work_dir = "/scratch/jgrogan/stack-working/study/"
+f = open(work_dir + "/study_collection.p", 'r')
+study_collection = pickle.load(f)
+skeleton_to_vtp(work_dir, study_collection)

test/get_tumour_stats.py

@@ -0,0 +1,114 @@
+import pickle
+import vtk
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+from stack3d.study.components import StudyData, MouseData, TimepointData
+import stack3d.formats.unet
+
+def get_time(path):
+    
+    no_space = path.replace(" ", "")
+    day_index = no_space.find("Day")
+    day_string = no_space[day_index+3:day_index+5]
+    day_string = day_string.replace("_", "")
+    return int(day_string)
+
+def render_skeleton(work_dir, study_collection):
+
+    for eachStudy in study_collection:
+        print "Rendering Study: ", eachStudy.raw_data_path
+        study_dir = work_dir + "/" + eachStudy.raw_data_path
+        
+        rad_fig, rad_ax = plt.subplots()
+        line_fig, line_ax = plt.subplots()
+        den_fig, den_ax = plt.subplots()
+        
+        for eachMouse in eachStudy.mice:
+            print "Rendering Mouse: ", eachMouse.raw_data_path
+            mouse_dir = study_dir + "/" + eachMouse.raw_data_path
+            
+            days = []
+            radii = []
+            lengths = []
+            densities = []
+            for eachTimePoint in eachMouse.timepoints:
+                days.append(get_time(eachTimePoint.raw_data_path))
+            if len(days) > 0:
+                days, eachMouse.timepoints = (list(t) for t in zip(*sorted(zip(days, eachMouse.timepoints))))            
+            
+            for kdx, eachTimePoint in enumerate(eachMouse.timepoints):
+                print "Rendering Time: ", eachTimePoint.raw_data_path
+                time_dir = mouse_dir + "/" + eachTimePoint.raw_data_path
+                base_path = "/analysis_analysis/skeleton.vtp"
+                if os.path.isfile(time_dir + base_path):
+                    reader = vtk.vtkXMLPolyDataReader()
+                    reader.SetFileName(time_dir + base_path)
+                    reader.Update()
+                    polydata = reader.GetOutput()
+                    
+                    for idx in range(polydata.GetNumberOfPoints()):
+                        loc = list(polydata.GetPoint(idx))
+                        loc[2] = 0
+                        polydata.GetPoints().SetPoint(idx, loc)
+                        
+                    lines = polydata.GetLines()
+                    points = polydata.GetPoints()
+                    length = 0.0
+                    for jdx in range(polydata.GetNumberOfCells()):
+                        pt_ids = vtk.vtkIdList()
+                        lines.GetCell(jdx, pt_ids)
+                        if pt_ids.GetNumberOfIds() == 2:
+                            pt0 = np.array(points.GetPoint(pt_ids.GetId(0)))
+                            pt1 = np.array(points.GetPoint(pt_ids.GetId(0)))
+                            length += np.linalg.norm(pt0-pt1)
+                    lengths.append(length)
+
+                    delaunay = vtk.vtkDelaunay2D()
+                    delaunay.SetInputData(polydata)
+                    delaunay.Update()
+
+                    com = vtk.vtkCenterOfMass()
+                    com.SetInputData(delaunay.GetOutput())
+                    com.SetUseScalarsAsWeights(False)
+                    com.Update()
+                    centre = com.GetCenter()
+
+                    feature = vtk.vtkFeatureEdges()
+                    feature.SetBoundaryEdges(1)
+                    feature.SetFeatureEdges(0)
+                    feature.SetNonManifoldEdges(0)
+                    feature.SetManifoldEdges(0)
+                    feature.SetInputData(delaunay.GetOutput())
+                    feature.Update()
+                    
+                    av_distance = 0.0
+                    for idx in range(feature.GetOutput().GetNumberOfPoints()):
+                        loc = feature.GetOutput().GetPoint(idx)
+                        av_distance += np.linalg.norm(np.array(centre)-np.array(loc))
+                    av_distance /= float(feature.GetOutput().GetNumberOfPoints())
+                    densities.append(length/(np.pi*av_distance*av_distance))
+                    
+                    print "d: ", days[kdx], "c: ", centre, "r: ", av_distance
+                    radii.append(av_distance)
+                else:
+                    radii.append(0)
+            rad_ax.plot(days, radii, lw=2.0, label=eachMouse.raw_data_path)
+            line_ax.plot(days, lengths, lw=2.0, label=eachMouse.raw_data_path)
+            den_ax.plot(days, densities, lw=2.0, label=eachMouse.raw_data_path)
+
+            handles, labels = rad_ax.get_legend_handles_labels()
+            rad_ax.legend(handles, labels)
+            handles, labels = line_ax.get_legend_handles_labels()
+            line_ax.legend(handles, labels)
+            handles, labels = den_ax.get_legend_handles_labels()
+            den_ax.legend(handles, labels)
+            
+        rad_fig.savefig(study_dir+"/timeline_radius.png", bbox_inches='tight', dpi=160)
+        line_fig.savefig(study_dir+"/timeline_length.png", bbox_inches='tight', dpi=160)
+        den_fig.savefig(study_dir+"/timeline_density.png", bbox_inches='tight', dpi=160)
+
+work_dir = "/scratch/jgrogan/stack-working/study/"
+f = open(work_dir + "/study_collection.p", 'r')
+study_collection = pickle.load(f)
+render_skeleton(work_dir, study_collection)

test/merge_plots.py

@@ -4,46 +4,91 @@ from PIL import Image
 from stack3d.study.components import StudyData, MouseData, TimepointData
 
 
+def get_time(path):
+    
+    no_space = path.replace(" ", "")
+    day_index = no_space.find("Day")
+    day_string = no_space[day_index+3:day_index+5]
+    day_string = day_string.replace("_", "")
+    return int(day_string)
+
 def merge_plots(work_dir, study_collection):
 
+    plot_name = "diameterPlot"
+    plot_name = "histogramDiameter"
+    plot_name = "rendering"
+    reduction_factor = 1
+    reduction_factor2 = 1
+
     for eachStudy in study_collection:
         print "Merging Study: ", eachStudy.raw_data_path
         study_dir = work_dir + "/" + eachStudy.raw_data_path
+        merge_paths = []
         for eachMouse in eachStudy.mice:
             print "Merging Mouse: ", eachMouse.raw_data_path
             mouse_dir = study_dir + "/" + eachMouse.raw_data_path
 
             image_paths = []
+            # first sort time points
+            days = []
+            for eachTimePoint in eachMouse.timepoints:
+                days.append(get_time(eachTimePoint.raw_data_path))
+            if len(days) > 0:
+                days, eachMouse.timepoints = (list(t) for t in zip(*sorted(zip(days, eachMouse.timepoints))))
+
             for eachTimePoint in eachMouse.timepoints:
                 time_dir = mouse_dir + "/" + eachTimePoint.raw_data_path
-                base_path = "/analysis_analysis/plots/vessels/diameterPlot.png"
+                #base_path = "/analysis_analysis/plots/vessels/" + plot_name + ".png"
+                base_path = "/analysis_analysis/histograms/" + plot_name + ".png"
+                base_path = "/analysis_analysis//" + plot_name + ".tiff"
                 if os.path.isfile(time_dir + base_path):
                     image_paths.append(time_dir + base_path)
 
-            images = map(Image.open, image_paths)
+            merge_path = mouse_dir + "/timeline_" + plot_name + ".jpg"
-            merge_path = mouse_dir + "/timeline_diameterPlot.jpg"
             merge_axis = 0
             print "Merging plots to: ", merge_path
-            if len(images) > 0:
+
-                widths, heights = zip(*(i.size for i in images))
+            if len(image_paths) > 0:
-                if merge_axis == 0:
+
-                    total_width = sum(widths)
+                widths = []
-                    max_height = max(heights)
+                heights = []
-                    new_im = Image.new('RGB', (total_width, max_height))
+                for path in image_paths:
-                    x_offset = 0
+                    im = Image.open(path)
-                    for im in images:
+                    widths.append(im.size[0])
-                        new_im.paste(im, (x_offset, 0))
+                    heights.append(im.size[1])
-                        x_offset += im.size[0]
+                    im.close()
-                    new_im.save(merge_path, optimize=True, quality=5)
+                total_width = int(0.5*sum(widths))
-                else:
+                max_height = int(0.8*max(heights))
-                    max_width = max(widths)
+                new_im = Image.new('RGB', (total_width, max_height))
-                    total_height = sum(heights)
+                x_offset = 0
-                    new_im = Image.new('RGB', (max_width, total_height))
+                for path in image_paths:
-                    y_offset = 0
+                    im = Image.open(path)
-                    for im in images:
+                    img2 = im.crop((int(0.25*im.size[0]), int(0.2*im.size[1]), int(0.75*im.size[0]), im.size[1]))
-                        new_im.paste(im, (0, y_offset))
+                    new_im.paste(img2, (x_offset, 0))
-                        y_offset += im.size[1]
+                    x_offset += int(0.5*im.size[0])
-                    new_im.save(merge_path, optimize=True, quality=5)
+                    im.close()
+                new_im.thumbnail((total_width/reduction_factor, max_height/reduction_factor))
+                merge_paths.append(merge_path)
+                new_im.save(merge_path)
+        if len(merge_paths) > 0:
+            widths = []
+            heights = []
+            for path in merge_paths:
+                im = Image.open(path)
+                widths.append(im.size[0])
+                heights.append(im.size[1])
+                im.close()
+            max_width = max(widths)
+            total_height = sum(heights)
+            new_im = Image.new('RGB', (max_width, total_height))
+            y_offset = 0
+            for path in merge_paths:
+                im = Image.open(path)
+                new_im.paste(im, (0, y_offset))
+                y_offset += im.size[1]
+                im.close()
+            new_im.thumbnail((max_width/reduction_factor2, total_height/reduction_factor2))
+            new_im.save(study_dir + "/timeline_" + plot_name + ".jpg")
 
 
 work_dir = "/scratch/jgrogan/stack-working/study/"

test/render_networks.py

@@ -1,10 +1,107 @@
+import pickle
 import vtk
+import os
+from stack3d.study.components import StudyData, MouseData, TimepointData
 import stack3d.formats.unet
 
-path = "/home/grogan/stack-working/skeleton.pkl"
-network_vtk = stack3d.formats.unet.skeleton_to_vtp(path)
 
-writer = vtk.vtkXMLPolyDataWriter()
+def render_skeleton(work_dir, study_collection):
-writer.SetInputData(network_vtk)
+
-writer.SetFileName("/home/grogan/test.vtp")
+    for eachStudy in study_collection:
-writer.Write()
+        print "Rendering Study: ", eachStudy.raw_data_path
+        study_dir = work_dir + "/" + eachStudy.raw_data_path
+        for eachMouse in eachStudy.mice:
+            print "Rendering Mouse: ", eachMouse.raw_data_path
+            mouse_dir = study_dir + "/" + eachMouse.raw_data_path
+            for eachTimePoint in eachMouse.timepoints:
+                print "Rendering Time: ", eachTimePoint.raw_data_path
+                time_dir = mouse_dir + "/" + eachTimePoint.raw_data_path
+                base_path = "/analysis_analysis/skeleton.vtp"
+                if os.path.isfile(time_dir + base_path):
+                    reader = vtk.vtkXMLPolyDataReader()
+                    reader.SetFileName(time_dir + base_path)
+                    reader.Update()
+                    polydata = reader.GetOutput()
+                    
+                    cell_to_point = vtk.vtkCellDataToPointData()
+                    cell_to_point.SetInputData(polydata)
+                    cell_to_point.Update()
+
+                    tubes = vtk.vtkTubeFilter()
+                    tubes.SetInputData(cell_to_point.GetOutput())
+                    tubes.SetNumberOfSides(6)
+                    tubes.SetRadius(1.0)
+                    tubes.SetRadiusFactor(50.0)
+                    tubes.SetVaryRadiusToVaryRadiusByScalar()
+                    tubes.Update()
+
+                    mapper = vtk.vtkPolyDataMapper()
+                    mapper.SetInputData(tubes.GetOutput())
+                    mapper.ScalarVisibilityOff()
+
+                    actor = vtk.vtkActor()
+                    actor.SetMapper(mapper)
+                    actor.GetProperty().SetColor(1, 0, 0)
+                    
+                    textActor = vtk.vtkTextActor()
+                    textActor.SetTextScaleModeToProp()
+                    textActor.SetDisplayPosition(400, 50)
+                    
+                    inp_string = "Study: " + eachStudy.raw_data_path
+                    inp_string += " | Mouse: " + eachMouse.raw_data_path
+                    inp_string += " | Time: " + eachTimePoint.raw_data_path
+                    
+                    textActor.SetInput(inp_string)
+                    tprop = textActor.GetTextProperty()
+                    tprop.SetFontSize(24)
+                    tprop.SetFontFamilyToArial()
+                    tprop.SetJustificationToCentered()
+                    tprop.BoldOn()
+                    tprop.ItalicOn()
+                    tprop.ShadowOn()
+                    tprop.SetColor(0, 0, 1)
+
+                    cubesource = vtk.vtkCubeSource()
+                    cubesource.SetBounds(0, 4000, 0, 4000, 0, 70)
+                    cubesource.Update()
+                    cube_mapper = vtk.vtkPolyDataMapper()
+                    cube_mapper.SetInputConnection(cubesource.GetOutputPort())
+                    cube_mapper.ScalarVisibilityOff()
+                    cube_actor = vtk.vtkActor()
+                    cube_actor.SetMapper(cube_mapper)
+                    cube_actor.GetProperty().SetColor(0, 0, 0)
+                    cube_actor.GetProperty().SetOpacity(0.1)
+
+                    # Create a renderer, render window, and interactor
+                    renderer = vtk.vtkRenderer()
+                    renderer.SetBackground(1, 1, 1)
+                    renderer.AddActor2D(textActor)
+                    #renderer.GetActiveCamera().Zoom(1.0)
+                    renderWindow = vtk.vtkRenderWindow()
+                    renderWindow.SetSize(1200, 800)
+                    renderWindow.SetAlphaBitPlanes(1)
+                    renderWindow.AddRenderer(renderer)
+#                     renderWindowInteractor = vtk.vtkRenderWindowInteractor()
+#                     renderWindowInteractor.SetRenderWindow(renderWindow)
+                    # Add the actors to the scene
+                    renderer.AddActor(actor)
+                    renderer.AddActor(cube_actor)
+                    renderer.ResetCameraClippingRange()
+                    # Render and interact
+                    renderWindow.Render()
+                    #renderWindowInteractor.Start()
+
+                    window_to_image_filter = vtk.vtkWindowToImageFilter()
+                    window_to_image_filter.SetInput(renderWindow)
+                    window_to_image_filter.SetMagnification(1);
+                    window_to_image_filter.SetInputBufferTypeToRGBA()
+                    window_to_image_filter.ReadFrontBufferOff()
+                    writer = vtk.vtkTIFFWriter()
+                    writer.SetInputConnection(window_to_image_filter.GetOutputPort())
+                    writer.SetFileName(time_dir + "/analysis_analysis/rendering.tiff")
+                    writer.Write()
+
+work_dir = "/scratch/jgrogan/stack-working/study/"
+f = open(work_dir + "/study_collection.p", 'r')
+study_collection = pickle.load(f)
+render_skeleton(work_dir, study_collection)