from catmaid.control.stack import get_stack_info
from catmaid.control.neurohdf import extract_as_numpy_array
import numpy as np
project_id = 1
stack_id = 3
skeleton_id = 1443
# retrieve all components for a given skeleton id
components = Component.objects.filter(project=project_id,
stack=stack_id,
skeleton_id=skeleton_id).all()
# retrieve stack information
stack_info = get_stack_info(project_id, stack_id)
# compute the skeleton bounding box
minX, minY = int(stack_info['dimension']['x']), int(
stack_info['dimension']['y'])
maxX, maxY = 0, 0
minZ, maxZ = int(stack_info['dimension']['z']), 0
for comp in components:
minX = min(minX, comp.min_x)
minY = min(minY, comp.min_y)
minZ = min(minZ, comp.z)
maxX = max(maxX, comp.max_x)
maxY = max(maxY, comp.max_y)
maxZ = max(maxZ, comp.z)
print 'found bounding box', minX, minY, maxX, maxY, minZ, maxZ
import numpy as np
project_id = 1
stack_id = 3
skeleton_id = 1443
# retrieve all components for a given skeleton id
components = Component.objects.filter(
project = project_id,
stack = stack_id,
skeleton_id = skeleton_id
).all()
# retrieve stack information
stack_info = get_stack_info( project_id, stack_id )
# compute the skeleton bounding box
minX, minY = int(stack_info['dimension']['x']), int(stack_info['dimension']['y'])
maxX, maxY = 0,0
minZ, maxZ = int(stack_info['dimension']['z']), 0
for comp in components:
minX = min(minX, comp.min_x)
minY = min(minY, comp.min_y)
minZ = min(minZ, comp.z)
maxX = max(maxX, comp.max_x)
maxY = max(maxY, comp.max_y)
maxZ = max(maxZ, comp.z)
print 'found bounding box', minX, minY, maxX, maxY, minZ, maxZ
def create_segmentation_neurohdf_file(request, project_id, stack_id):
filename=os.path.join( settings.HDF5_STORAGE_PATH, '{0}_{1}_segmentation.hdf'.format( project_id, stack_id ) )
print >> sys.stderr, filename
with closing(h5py.File(filename, 'w')) as hfile:
hfile.attrs['neurohdf_version'] = '0.1'
scaleGroup = hfile.create_group("scale")
scale_zero = scaleGroup.create_group("0")
sectionGroup = scale_zero.create_group("section")
# retrieve stack information to transform world coordinates to pixel coordinates
stack_info = get_stack_info( project_id, stack_id, request.user )
width=stack_info['dimension']['x']
height=stack_info['dimension']['y']
stack = get_object_or_404(Stack, pk=stack_id)
project = get_object_or_404(Project, pk=project_id)
whitelist = range( int(stack_info['dimension']['z']) )
[whitelist.remove( int(k) ) for k,v in stack_info['broken_slices'].items()]
# retrieve all skeletons that have a component associated with it in order
# to define a globally consistent colormap from skeleton_id to color
all_components_with_skeletons = Component.objects.filter(
project = project,
stack = stack,
skeleton_id__isnull=False
).distinct('skeleton_id')
all_skeletons = [ele.skeleton_id for ele in all_components_with_skeletons]
# TODO: check that no colors are duplicate
colors = np.random.randint (0,256, (len(all_skeletons),3) )
colormap = dict(zip(all_skeletons, colors))
for z in whitelist:
section = sectionGroup.create_group(str(z))
shape=(height,width)
skeletonIdsPixelArray=np.zeros(shape, dtype=np.long)
skeletonIdsPixelArrayRGB=np.zeros( (height,width, 3), dtype=np.uint8 )
### Write all the components
all_components = Component.objects.filter(
project = project,
stack = stack,
z=z
).order_by('creation_time').all()
for comp in all_components:
x,y = get_pixellist_for_component(project_id, stack_id, z, comp.component_id)
skeletonIdsPixelArray[y,x] = comp.skeleton_id
skeletonIdsPixelArrayRGB[y,x,:] = colormap[comp.skeleton_id]
all_free_drawings = Drawing.objects.filter(
stack=stack,
project=project,
z = z).exclude(component_id__isnull=False).all()
for freeDrawing in all_free_drawings:
typename = DrawingTypesId[freeDrawing.type]
print >> sys.stderr, 'freedrawing type', freeDrawing.type, typename
x, y = get_indices_for_drawing(freeDrawing, width, height)
# TODO: erasor should only delete pixels of its corresponding skeleton_id
if freeDrawing.type == DrawingTypes['soma']['value']:
skeletonIdsPixelArray[y,x] = freeDrawing.skeleton_id
skeletonIdsPixelArrayRGB[y,x,:] = colormap[freeDrawing.skeleton_id]
else:
skeletonIdsPixelArray[y,x] = DrawingTypes[typename]['value']
skeletonIdsPixelArrayRGB[y,x,:] = DrawingTypesColormap[typename]
### Write out
section.create_dataset("skeletons", data=skeletonIdsPixelArray, compression='gzip', compression_opts=1)
# map to color
section.create_dataset("skeletons_rgb", data=skeletonIdsPixelArrayRGB, compression='gzip', compression_opts=1)
return
