Add initial batch processing and do some tidying.

.project

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>Stack3D</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.python.pydev.PyDevBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.python.pydev.pythonNature</nature>
+	</natures>
+</projectDescription>

.pydevproject

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<?eclipse-pydev version="1.0"?><pydev_project>
+<pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
+<path>/${PROJECT_DIR_NAME}</path>
+</pydev_pathproperty>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.7</pydev_property>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>
+</pydev_project>

.settings/org.eclipse.core.resources.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+encoding//src/stack3d/formats/ome_schema.py=utf-8

process_russ_format.py

@@ -1,44 +0,0 @@
-"""
-Reader for the MATLAB vessel network format provided by Russel Bates (russell.bates@new.ox.ac.uk)
-"""
-
-from argparse import ArgumentParser
-import scipy.io
-import numpy as np
-
-def compare(x, y):
-    
-    return (x[0] == y[0]) and (x[1] == y[1]) and (x[2] == y[2])
-
-def convert_to_vtk(mat): 
-    
-    """
-    Convert the format to VTK
-    """
-    
-    nodes = []
-    edges = []
-    
-    for idx, eachConnectedComponent in enumerate(mat["Vessels"][0]):
-        adjacency = eachConnectedComponent['Adj']
-        branches  = eachConnectedComponent['Branch'][0][0][0]
-        if idx ==0:
-            for kdx, eachBranch in enumerate(branches):
-                if kdx <200:
-                    for jdx, eachPoint in enumerate(eachBranch['Points'][0][0]):
-                        nodes.append(np.array(eachPoint))
-                        
-    for idx, eachEntry in enumerate(nodes):
-        for jdx, eachOtherEntry in enumerate(nodes):
-            if idx!=jdx:
-                if compare(eachEntry, eachOtherEntry):
-                    print eachEntry, eachOtherEntry, idx, jdx
-                    break
-        
-            #nodes.append(eachBranch['Points'][0][0][0])
-            #print eachBranch['Points'][0][0][0]
-            #adjacency_indices = adjacency[0][0].nonzero()
-            #print adjacency_indices[0]
-
-mat = scipy.io.loadmat('/home/grogan/Vessels.mat', struct_as_record=True)
-convert_to_vtk(mat)

src/stack3d/formats/unet.py

@@ -0,0 +1,136 @@
+""" Format conversion for Russ Bate's unet format.
+"""
+
+from __future__ import print_function
+import inspect
+import os
+import csv
+from subprocess import call
+from argparse import ArgumentParser
+import scipy.io
+import networkx as nx
+import stack3d.formats
+
+
+def load_skeleton(path):
+
+    """
+    Load the skeleton from a pickle
+    """
+
+    # Delayed import so script can be run with both Python 2 and 3
+    from unet_core.vessel_analysis import VesselTree
+
+    v = VesselTree()
+    v.load_skeleton(path)
+    return v.skeleton
+
+
+def skeleton_to_vtp(path):
+
+    temp_output_path = os.path.dirname(os.path.realpath(path)) + "/temp_network_csv.csv"
+    script_path = inspect.getfile(stack3d.formats.unet).replace(".pyc", ".py")
+    launch_args = " --input '" + path + "' --output '" + temp_output_path + "' --format csv --field diameter"
+    call("python3 " + script_path + launch_args, shell=True)
+
+    # Avoid vtk import when method not used to reduce dependency overhead
+    import vtk
+    polydata = vtk.vtkPolyData()
+    points = vtk.vtkPoints()
+    cells = vtk.vtkCellArray()
+    data = vtk.vtkDoubleArray()
+
+    with open(temp_output_path, 'rb') as csvfile:
+        reader = csv.reader(csvfile, delimiter=',', quotechar='|')
+        counter = 0
+        first = 0
+        for row in reader:
+            if first == 0:
+                first += 1
+                continue
+            point0 = [float(x) for x in row[0:3]]
+            point1 = [float(x) for x in row[3:6]]
+            diameter = float(row[6])
+            points.InsertNextPoint(point0)
+            points.InsertNextPoint(point1)
+            line = vtk.vtkLine()
+            line.GetPointIds().SetId(0, counter)
+            line.GetPointIds().SetId(1, counter+1)
+            counter += 2
+            cells.InsertNextCell(line)
+            data.InsertNextTuple1(diameter)
+
+        polydata.SetPoints(points)
+        polydata.SetLines(cells)
+        polydata.GetCellData().SetScalars(data)
+
+        clean = vtk.vtkCleanPolyData()
+        clean.SetInputData(polydata)
+        clean.Update()
+
+        return clean.GetOutput()
+
+
+def skeleton_to_matlab(skeleton, field, output_path):
+
+    """
+    Convert the skeleton's network description to matlab sparse matrix format.
+    Each mat file corresponds to a connected component
+    """
+
+#     if os.path.isabs(output_path) and not os.path.exists(output_path):
+#         os.makedirs(output_path)
+
+    for idx, component in enumerate(skeleton.components):
+        for n, nbrs in component.graph.adjacency_iter():
+            for nbr, edict in nbrs.items():
+                branch = edict[0]["branch"]
+                component.graph.add_edge(n, nbr, weight=branch.diameter)
+        scipy_mat = nx.to_scipy_sparse_matrix(component.graph)
+        output = {"skeleton": scipy_mat}
+        output_file = output_path + "/skeleton_" + field + "_Comp_" + str(idx) + ".mat"
+        scipy.io.savemat(output_file, output)
+
+def skeleton_to_csv(skeleton, output_path):
+
+    """
+    Convert the skeleton's network description to csv format
+    """
+
+#     if os.path.isabs(output_path) and not os.path.exists(output_path):
+#         os.makedirs(output_path)
+
+    f = open(output_path, "w")
+    f.write("P0 - x, P0 - y, P0 - z, P1 - x, P1 - y, P1 - z, diameter")
+
+    for _, _, branch in skeleton.skeleton_branch_iter():
+        for idx, p1 in enumerate(branch.points):
+            if idx > 0:
+                p0 = branch.points[idx-1]
+                p0_s = str(p0.x) + "," + str(p0.y) + "," + str(p0.z)
+                p1_s = str(p1.x) + "," + str(p1.y) + "," + str(p1.z)
+                f.write(p0_s + "," + p1_s + "," + str(branch.diameter) + "\n")
+    f.close()
+
+
+if __name__ == "__main__":
+
+    parser = ArgumentParser()
+    parser.add_argument('--input', type=str, help='Input skeleton file.')
+    parser.add_argument('--output', type=str, help='Output directory.')
+    parser.add_argument('--format', type=str,
+                        help='Output format.',
+                        choices=['csv', 'mat'],
+                        default='mat')
+    parser.add_argument('--field', type=str,
+                        help='Output field.',
+                        choices=['diameter', "length", "tortuosity"],
+                        default='diameter')
+    args = parser.parse_args()
+
+    skeleton = load_skeleton(args.input)
+    if "csv" in args.format:
+        skeleton_to_csv(skeleton, args.output)
+    elif "mat" in args.format:
+        skeleton_to_matlab(skeleton, args.field, args.output)
+    

src/stack3d/formats/zeiss.py

@@ -1,3 +1,4 @@
+
 """
 Conversion of IMS/LSM/CZI files to OME and then Generic TIFFs
 """

src/stack3d/study/components.py

@@ -0,0 +1,22 @@
+class TimepointData(object):
+
+    def __init__(self):
+
+        self.raw_data_path = None
+
+
+class MouseData(object):
+
+    def __init__(self):
+
+        self.raw_data_path = None
+        self.extra_path = ""
+        self.timepoints = []
+
+
+class StudyData(object):
+
+    def __init__(self):
+
+        self.raw_data_path = None
+        self.mice = []

src/stack3d/viewing/simple_render.py

@@ -9,10 +9,10 @@ import mp_color_map
 
 def get_ox_map():
 
-    files = ["/home/grogan/oxygen_solution_loc_0.vti",
+    files = ["/home/grogan/oxygen_solution_loc_1.vti",
-             "/home/grogan/oxygen_solution_loc_1.vti",
              "/home/grogan/oxygen_solution_loc_2.vti",
-             "/home/grogan/oxygen_solution_loc_3.vti"]
+             "/home/grogan/oxygen_solution_loc_3.vti",
+             "/home/grogan/oxygen_solution_loc_4.vti"]
     offsets = [(0.0,0.0), (40.0, 0.0), (40.0, 40.0), (0.0, 40.0)]
     
     ox_actors = []
@@ -72,12 +72,12 @@ def get_ox_map():
         ox_actor = vtk.vtkActor()
         ox_actor.SetMapper(ox_mapper)
         ox_actor.GetProperty().SetColor(0.0, 1.0, 0.0)
-        ox_actor.GetProperty().SetOpacity(0.5)
+        ox_actor.GetProperty().SetOpacity(0.8)
         ox_actors.append(ox_actor)
 
     scale_bar = vtk.vtkScalarBarActor()
     scale_bar.SetLookupTable(scaled_ctf);
-    #scale_bar.SetTitle("Oxygen Tension (mmHg)");
+    scale_bar.SetTitle(".");
     scale_bar.SetOrientationToVertical();
     scale_bar.GetPositionCoordinate().SetCoordinateSystemToNormalizedViewport();
     scale_bar.GetPositionCoordinate().SetValue(0.23, 0.27);
@@ -95,7 +95,7 @@ def get_ox_map():
     scale_bar.GetTitleTextProperty().SetFontSize(15)
     scale_bar.GetLabelTextProperty().SetFontSize(15)
     scale_bar.GetTitleTextProperty().SetColor(1.0, 1.0, 1.0);
-    scale_bar.GetLabelTextProperty().SetColor(1.0, 1.0, 1.0);
+    scale_bar.GetLabelTextProperty().SetColor(0.0, 0.0, 0.0);
     
     return ox_actors, scale_bar
 
@@ -175,8 +175,7 @@ def render_image(image_path, threshold = 20.0):
             input_files.append(image_path + "/"+eachFile)
     
     renderer = vtk.vtkRenderer()
-    renderer.SetBackground(20.0/255.0,30.0/255.0,48.0/255.0);
+    renderer.SetBackground(1.0,1.0,1.0);
-    renderer.SetBackground2(36.0/255.0,59.0/255.0,85.0/255.0);
     
     for eachImage in input_files:
         reader= vtk.vtkXMLImageDataReader()
@@ -198,7 +197,7 @@ def render_image(image_path, threshold = 20.0):
         opacity_transfer_func.AddPoint(0, 0.0 )
         opacity_transfer_func.AddPoint(threshold-1.0, 0.0 )
         #opacity_transfer_func.AddPoint(threshold, 1.0 )
-        opacity_transfer_func.AddPoint(255.0, 0.1 )
+        opacity_transfer_func.AddPoint(255.0, 1.0 )
         
         volume_properties = vtk.vtkVolumeProperty()
         volume_properties.SetColor( color_transfer_func )
@@ -230,7 +229,9 @@ def render_image(image_path, threshold = 20.0):
     render_window.AddRenderer(renderer)
     window_interactor.SetRenderWindow(render_window)
     
-    render_window.SetSize(170, 177)
+    render_window.SetSize(1200, 800)
+    render_window.SetAlphaBitPlanes(1)
+ 
     render_window.Render()
     ox_actors, scale_bar_actor = get_ox_map()
     #renderer.AddActor(scale_bar_actor)
@@ -247,14 +248,16 @@ def render_image(image_path, threshold = 20.0):
     
     window_to_image_filter = vtk.vtkWindowToImageFilter()
     window_to_image_filter.SetInput(render_window)
+    window_to_image_filter.SetMagnification(1);
+    window_to_image_filter.SetInputBufferTypeToRGBA()
+    window_to_image_filter.ReadFrontBufferOff()
     writer = vtk.vtkTIFFWriter()
     extension = ".tiff"
     writer.SetInputConnection(window_to_image_filter.GetOutputPort())
     writer.SetFileName("vtk_animation_0"+extension)
     writer.Write()
      
-     
+    num_samples = 2
-    num_samples = 1
     for idx in range(num_samples):
          
         if idx==0:
@@ -264,38 +267,42 @@ def render_image(image_path, threshold = 20.0):
         renderer.GetActiveCamera().OrthogonalizeViewUp()
         #time.sleep(0.02)
         
-        #renderer.GetActiveCamera().Dolly(1.002))
+        #renderer.GetActiveCamera().Elevation(-1.0)
+        renderer.GetActiveCamera().Dolly(1.002)
+        renderer.ResetCameraClippingRange()
         render_window.Render()
         window_to_image_filter.Modified()
         writer.SetFileName("vtk_animation_"+str(idx+1)+extension)
         writer.Write()
      
+    renderer.AddActor(scale_bar_actor)
+        
     renderer.RemoveActor(ox_actors[0])
     render_window.Render()
-    window_to_image_filter.Modified()
+#     window_to_image_filter.Modified()
-    writer.SetFileName("vtk_animation_"+str(num_samples+1)+extension)
+#     writer.SetFileName("vtk_animation_"+str(num_samples+1)+extension)
-    writer.Write()
+#     writer.Write()
-    
+#     
-    cell_actors = add_cells()
+#     cell_actors = add_cells()
-    renderer.AddActor(cell_actors[0])
+#     renderer.AddActor(cell_actors[0])
-    render_window.Render()
+#     render_window.Render()
-    window_to_image_filter.Modified()
+#     window_to_image_filter.Modified()
-    writer.SetFileName("vtk_animation_"+str(num_samples+2)+extension)
+#     writer.SetFileName("vtk_animation_"+str(num_samples+2)+extension)
-    writer.Write()
+#     writer.Write()
-    renderer.RemoveActor(cell_actors[0])
+#     renderer.RemoveActor(cell_actors[0])
-    
+#      
-    renderer.AddActor(cell_actors[1])
+#     renderer.AddActor(cell_actors[1])
-    render_window.Render()
+#     render_window.Render()
-    window_to_image_filter.Modified()
+#     window_to_image_filter.Modified()
-    writer.SetFileName("vtk_animation_"+str(num_samples+3)+extension)
+#     writer.SetFileName("vtk_animation_"+str(num_samples+3)+extension)
-    writer.Write()
+#     writer.Write()
-    renderer.RemoveActor(cell_actors[1])
+#     renderer.RemoveActor(cell_actors[1])
-    
+#      
-    renderer.AddActor(cell_actors[2])
+#     renderer.AddActor(cell_actors[2])
-    render_window.Render()
+#     render_window.Render()
-    window_to_image_filter.Modified()
+#     window_to_image_filter.Modified()
-    writer.SetFileName("vtk_animation_"+str(num_samples+4)+extension)
+#     writer.SetFileName("vtk_animation_"+str(num_samples+4)+extension)
-    writer.Write()
+#     writer.Write()
      
     window_interactor.Start()
     

test/merge_plots.py

@@ -0,0 +1,52 @@
+import os
+import pickle
+from PIL import Image
+from stack3d.study.components import StudyData, MouseData, TimepointData
+
+
+def merge_plots(work_dir, study_collection):
+
+    for eachStudy in study_collection:
+        print "Merging Study: ", eachStudy.raw_data_path
+        study_dir = work_dir + "/" + eachStudy.raw_data_path
+        for eachMouse in eachStudy.mice:
+            print "Merging Mouse: ", eachMouse.raw_data_path
+            mouse_dir = study_dir + "/" + eachMouse.raw_data_path
+
+            image_paths = []
+            for eachTimePoint in eachMouse.timepoints:
+                time_dir = mouse_dir + "/" + eachTimePoint.raw_data_path
+                base_path = "/analysis_analysis/plots/vessels/diameterPlot.png"
+                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_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 merge_axis == 0:
+                    total_width = sum(widths)
+                    max_height = max(heights)
+                    new_im = Image.new('RGB', (total_width, max_height))
+                    x_offset = 0
+                    for im in images:
+                        new_im.paste(im, (x_offset, 0))
+                        x_offset += im.size[0]
+                    new_im.save(merge_path, optimize=True, quality=5)
+                else:
+                    max_width = max(widths)
+                    total_height = sum(heights)
+                    new_im = Image.new('RGB', (max_width, total_height))
+                    y_offset = 0
+                    for im in images:
+                        new_im.paste(im, (0, y_offset))
+                        y_offset += im.size[1]
+                    new_im.save(merge_path, optimize=True, quality=5)
+
+
+work_dir = "/scratch/jgrogan/stack-working/study/"
+f = open(work_dir + "/study_collection.p", 'r')
+study_collection = pickle.load(f)
+merge_plots(work_dir, study_collection)

test/render_networks.py

@@ -0,0 +1,10 @@
+import vtk
+import stack3d.formats.unet
+
+path = "/home/grogan/stack-working/skeleton.pkl"
+network_vtk = stack3d.formats.unet.skeleton_to_vtp(path)
+
+writer = vtk.vtkXMLPolyDataWriter()
+writer.SetInputData(network_vtk)
+writer.SetFileName("/home/grogan/test.vtp")
+writer.Write()

test/skeleton_to_mat.py

@@ -0,0 +1,55 @@
+import os
+import inspect
+import pickle
+from subprocess import call
+from PIL import Image
+import vtk
+import scipy.sparse as sps
+from scipy.io import savemat
+from stack3d.study.components import StudyData, MouseData, TimepointData
+import stack3d.formats.unet
+
+
+def vtk_to_mat(polydata, path):
+
+    num_points = polydata.GetNumberOfPoints()
+    sps_acc = sps.coo_matrix((num_points, num_points))
+    data = []
+    row_indices = []
+    column_indices = []
+    lines = polydata.GetLines()
+    vtk_data = polydata.GetCellData().GetScalars()
+    
+    print "np: ", num_points
+    for idx in range(lines.GetNumberOfCells()):
+        points = vtk.vtkIdList()
+        lines.GetCell(idx, points)
+        if points.GetNumberOfIds() == 2:
+            row_indices.append(points.GetId(0))
+            column_indices.append(points.GetId(1))
+            data.append(vtk_data.GetTuple1(idx))
+    sps_acc = sps_acc + sps.coo_matrix((data, (row_indices, column_indices)), shape=(num_points, num_points))
+    savemat(path, {'skeleton': sps_acc})
+
+
+def skeleton_to_mat(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_distance.mat"))
+                    polydata = stack3d.formats.unet.skeleton_to_vtp(time_dir + base_path)
+                    vtk_to_mat(polydata, output_path)
+
+work_dir = "/scratch/jgrogan/stack-working/study/"
+f = open(work_dir + "/study_collection.p", 'r')
+study_collection = pickle.load(f)
+skeleton_to_mat(work_dir, study_collection)

test/study_setup.py

@@ -0,0 +1,97 @@
+import os
+import pickle
+from distutils.dir_util import copy_tree
+from shutil import copyfile
+from stack3d.study.components import StudyData, MouseData, TimepointData
+
+
+def setup_study_collection_from_remote(path):
+
+    """Scan the remote directory structure. Remote needs to be mounted first
+    with Samba etc."""
+
+    study_collection = []
+    study_dirs = next(os.walk(path))[1]
+
+    for study_dir in study_dirs:
+        new_study = StudyData()
+        new_study.raw_data_path = study_dir
+        print "Set up study: ", study_dir
+        mouse_dirs = next(os.walk(path + "/" + study_dir))[1]
+        for mouse_dir in mouse_dirs:
+            new_mouse = MouseData()
+            new_mouse.raw_data_path = mouse_dir
+            print "Set up mouse: ", mouse_dir
+
+            cumulative_path = path + "/" + study_dir + "/" + mouse_dir
+            if os.path.isdir(cumulative_path + "/Outputs_new_model"):
+                new_mouse.extra_path = "/Outputs_new_model/"
+            elif os.path.isdir(cumulative_path + "/Outputs"):
+                new_mouse.extra_path = "/Outputs/"
+            timepoint_dirs = next(os.walk(cumulative_path + new_mouse.extra_path))[1]
+            for timepoint_dir in timepoint_dirs:
+                if "TIF" not in timepoint_dir:
+                    new_timepoint = TimepointData()
+                    new_timepoint.raw_data_path = timepoint_dir
+                    new_mouse.timepoints.append(new_timepoint)
+            new_study.mice.append(new_mouse)
+        study_collection.append(new_study)
+    return study_collection
+
+
+def setup_local_study_directory_structure(path, study_collection):
+
+    for eachStudy in study_collection:
+        study_dir = path + "/" + eachStudy.raw_data_path
+        if not os.path.exists(study_dir):
+            os.makedirs(study_dir)
+        for eachMouse in eachStudy.mice:
+            mouse_dir = study_dir + "/" + eachMouse.raw_data_path
+            if not os.path.exists(mouse_dir):
+                os.makedirs(mouse_dir)
+            for eachTimePoint in eachMouse.timepoints:
+                time_dir = mouse_dir + "/" + eachTimePoint.raw_data_path
+                if not os.path.exists(time_dir):
+                    os.makedirs(time_dir)
+
+
+def copy_files(remote_path, local_path, study_collection):
+
+    for eachStudy in study_collection:
+        print "Copying Study: ", eachStudy.raw_data_path
+        remote_study_dir = remote_path + "/" + eachStudy.raw_data_path
+        local_study_dir = local_path + "/" + eachStudy.raw_data_path
+        for eachMouse in eachStudy.mice:
+            print "Copying Mouse: ", eachMouse.raw_data_path
+            remote_mouse_dir = remote_study_dir + "/" + eachMouse.raw_data_path
+            local_mouse_dir = local_study_dir + "/" + eachMouse.raw_data_path
+            for eachTimePoint in eachMouse.timepoints:
+                remote_time_dir = remote_mouse_dir + eachMouse.extra_path + "/" + eachTimePoint.raw_data_path
+                local_time_dir = local_mouse_dir + "/" + eachTimePoint.raw_data_path
+
+                if os.path.isdir(remote_time_dir + "/analysis_analysis"):
+                    groups = ["csv", "histograms", "plots"]
+                    for group in groups:
+                        if os.path.isdir(remote_time_dir + "/analysis_analysis/" + group):
+                            copy_tree(remote_time_dir + "/analysis_analysis/" + group,
+                                      local_time_dir + "/analysis_analysis/" + group)
+
+                    if os.path.isfile(remote_time_dir + "/analysis_analysis/skeleton.pkl"):
+                        copyfile(remote_time_dir + "/analysis_analysis/skeleton.pkl", 
+                                 local_time_dir + "/analysis_analysis/skeleton.pkl")
+#             
+work_dir = "/scratch/jgrogan/stack-working/study/"
+
+samba_path = os.environ["XDG_RUNTIME_DIR"] + "/gvfs/"
+raw_data_path = samba_path + "smb-share:server=imcore1.rob.ox.ac.uk,share=maths"
+raw_data_path += "/Window Experiments/James/Network analysis/"
+
+# study_collection = setup_study_collection_from_remote(raw_data_path)
+# f = open(work_dir + "/study_collection.p", "wb")
+# pickle.dump(study_collection, f)
+
+f = open(work_dir + "/study_collection.p", 'r')
+study_collection = pickle.load(f)
+
+#setup_local_study_directory_structure(work_dir, study_collection)
+copy_files(raw_data_path, work_dir, study_collection)

utility.py

@@ -1,36 +0,0 @@
-"""
-Utilities for logging, parallel execution
-"""
-
-import os
-import logging
-
-def do_setup(tool_name = None):
-    
-    out_directory = os.getcwd() + "/Stack3D_Logging/"
-    if not os.path.exists(out_directory):
-        os.makedirs(out_directory)
-    if tool_name is not None:
-        filename = out_directory + tool_name + ".log"
-    else:
-        filename = out_directory + "/root.log"
-        
-    logging.basicConfig(level=logging.DEBUG,
-                format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s',
-                datefmt='%m-%d %H:%M',
-                filename=filename,
-                filemode='w')
-    
-    console = logging.StreamHandler()
-    console.setLevel(logging.INFO)
-    
-    # set a format which is simpler for console use
-    formatter = logging.Formatter('%(name)-12s: %(levelname)-8s %(message)s')
-    
-    # tell the handler to use this format
-    console.setFormatter(formatter)
-    
-    # add the handler to the root logger
-    logging.getLogger('').addHandler(console)
-        
-