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One mode ellipsoid #1158

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One mode ellipsoid #1158

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3de2b7a
Updating ellipsoid generation so user can specify which radii vary
jadie1 Mar 9, 2021
ad872cb
Changing data to ellipsoid_1mode
jadie1 Mar 9, 2021
1762396
Updating to use ellipsoid_1mode_aligned data
jadie1 Mar 9, 2021
a14d520
Updating fd to use ellipsoid_1mode data
jadie1 Mar 9, 2021
47e273f
Updating seg notebook to use ellipsoid_1mode
jadie1 Mar 9, 2021
914cf9d
Updating mesh notebook to use ellipsoid_1mode
jadie1 Mar 9, 2021
f0b2234
Updating exploring seg notebook to use ellipsoid_1mode
jadie1 Mar 9, 2021
d762441
Switching data on githib to ellipsoid_1mode.zip
jadie1 Mar 9, 2021
96985dc
updating grooming segmentation to use ellipsoid_1mode and updated sha…
iyerkrithika21 Mar 10, 2021
a4e7537
Updating doc version of shape cohort gen notebook
jadie1 Mar 10, 2021
3ea7651
Fixing LFS link for zip file.
akenmorris Mar 18, 2021
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3 changes: 0 additions & 3 deletions Examples/Python/Data/ellipsoid-v0.zip
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3 changes: 3 additions & 0 deletions Examples/Python/Data/ellipsoid_1mode.zip
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3 changes: 0 additions & 3 deletions Examples/Python/Data/ellipsoid_fd-v0.zip
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2 changes: 1 addition & 1 deletion Examples/Python/ellipsoid.py
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Expand Up @@ -28,7 +28,7 @@ def Run_Pipeline(args):
if int(args.interactive) != 0:
input("Press Enter to continue")
# Get data
datasetName = "ellipsoid-v1"
datasetName = "ellipsoid_1mode"
outputDirectory = "Output/ellipsoid/"
if not os.path.exists(outputDirectory):
os.makedirs(outputDirectory)
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2 changes: 1 addition & 1 deletion Examples/Python/ellipsoid_cut.py
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Expand Up @@ -26,7 +26,7 @@ def Run_Pipeline(args):
if int(args.interactive) != 0:
input("Press Enter to continue")
# Get data
datasetName = "ellipsoid_aligned-v1"
datasetName = "ellipsoid_1mode_aligned"
outputDirectory = "Output/ellipsoid_cut/"
if not os.path.exists(outputDirectory):
os.makedirs(outputDirectory)
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8 changes: 4 additions & 4 deletions Examples/Python/ellipsoid_fd.py
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Expand Up @@ -36,14 +36,14 @@ def Run_Pipeline(args):
if int(args.interactive) != 0:
input("Press Enter to continue")

datasetName = "ellipsoid_fd-v0"
datasetName = "ellipsoid_1mode"
outputDirectory = "Output/ellipsoid_fd/"
if not os.path.exists(outputDirectory):
os.makedirs(outputDirectory)
CommonUtils.download_and_unzip_dataset(datasetName, outputDirectory)

fileListDT = sorted(glob.glob(outputDirectory + datasetName + "/distance_transforms/*.nrrd"))
fileListNew = sorted(glob.glob(outputDirectory + datasetName + "/new_distance_transforms/*.nrrd"))
fileListDT = sorted(glob.glob(outputDirectory + datasetName + "/groomed/distance_transforms/*.nrrd"))
fileListNew = sorted(glob.glob(outputDirectory + datasetName + "/fd_segmentations/*.nrrd"))

"""
## GROOM : Data Pre-processing
Expand Down Expand Up @@ -86,7 +86,7 @@ def Run_Pipeline(args):
Evaluate the meanshape of the existing shape model and use that to initialize the
particles on the new shapes
"""
shapemodelDir = outputDirectory + datasetName + "/shape_models/pretrained/128/"
shapemodelDir = outputDirectory + datasetName + "/shape_models/ellipsoid/128/"
print(os.listdir(shapemodelDir))
findMeanShape(shapemodelDir)
meanShapePath = shapemodelDir + '/meanshape_local.particles'
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2 changes: 1 addition & 1 deletion Examples/Python/ellipsoid_mesh.py
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Expand Up @@ -24,7 +24,7 @@ def Run_Pipeline(args):
if int(args.interactive) != 0:
input("Press Enter to continue")

datasetName = "ellipsoid-v0"
datasetName = "ellipsoid_1mode_aligned"
outputDirectory = "Output/ellipsoid_mesh/"
if not os.path.exists(outputDirectory):
os.makedirs(outputDirectory)
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4 changes: 2 additions & 2 deletions Examples/Python/notebooks/tutorials/getting-started-with-exploring-segmentations.ipynb
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Expand Up @@ -298,7 +298,7 @@
"After you login, click `Collections` on the left panel and then `use-case-data-v2`. Select the dataset you would like to download by clicking on the checkbox on the left of the dataset name. See the video below.\n",
"After you download the dataset zip file, make sure you unzip/extract the contents in the appropriate location.\n",
"\n",
"**This notebook assumes that you have downloaded `ellipsoid-v1` and you have placed the unzipped folder `ellipsoid-v1` in `Examples/Python/Data`.** Feel free to use your own dataset. \n",
"**This notebook assumes that you have downloaded `ellipsoid_1mode` and you have placed the unzipped folder `ellipsoid_1mode` in `Examples/Python/Data`.** Feel free to use your own dataset. \n",
"\n",
"\n",
"<p><video src=\"https://sci.utah.edu/~shapeworks/doc-resources/mp4s/portal_data_download.mp4\" autoplay muted loop controls style=\"width:100%\"></p>"
Expand All @@ -311,7 +311,7 @@
"outputs": [],
"source": [
"# dataset name is the folder name for your dataset\n",
"datasetName = 'ellipsoid-v1'\n",
"datasetName = 'ellipsoid_1mode'\n",
"\n",
"# path to the dataset where we can find shape data \n",
"# here we assume shape data are given as binary segmentations\n",
Expand Down
4 changes: 2 additions & 2 deletions Examples/Python/notebooks/tutorials/getting-started-with-grooming-segmentations.ipynb
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Expand Up @@ -641,7 +641,7 @@
"After you login, click `Collections` on the left panel and then `use-case-data-v2`. Select the dataset you would like to download by clicking on the checkbox on the left of the dataset name. See the video below.\n",
"After you download the dataset zip file, make sure you unzip/extract the contents in the appropriate location.\n",
"\n",
"**This notebook assumes that you have downloaded `ellipsoid-v1` and you have placed the unzipped folder `ellipsoid-v1` in `Examples/Python/Data`.** Feel free to use your own dataset. \n",
"**This notebook assumes that you have downloaded `ellipsoid_1mode` and you have placed the unzipped folder `ellipsoid_1mode` in `Examples/Python/Data`.** Feel free to use your own dataset. \n",
"\n",
"\n",
"<p><video src=\"https://sci.utah.edu/~shapeworks/doc-resources/mp4s/portal_data_download.mp4\" autoplay muted loop controls style=\"width:100%\"></p>"
Expand All @@ -656,7 +656,7 @@
"import glob # for paths and file-directory search\n",
"from pathlib import Path # for generating robust paths irrespective of the platform:Win/Linux/Mac\n",
"# dataset name is the folder name for your dataset\n",
"datasetName = 'ellipsoid-v1'\n",
"datasetName = 'ellipsoid_1mode'\n",
"\n",
"# file extension for the shape data\n",
"shapeExtention = '.nrrd'\n",
Expand Down
4 changes: 2 additions & 2 deletions Examples/Python/notebooks/tutorials/getting-started-with-meshes.ipynb
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Expand Up @@ -128,7 +128,7 @@
"\n",
"After you login, click `Collections` on the left panel and then `use-case-data-v2`. Select the dataset you would like to download by clicking on the checkbox on the left of the dataset name. See the video below.\n",
"\n",
"**This notebook assumes that you have downloaded `ellipsoid-v1` and you have placed the unzipped folder`ellipsoid-v1`in `Examples/Python/Data`.** Feel free to use your own dataset. \n",
"**This notebook assumes that you have downloaded `ellipsoid_1mode` and you have placed the unzipped folder`ellipsoid_1mode`in `Examples/Python/Data`.** Feel free to use your own dataset. \n",
"\n",
"\n",
"<p><video src=\"https://sci.utah.edu/~shapeworks/doc-resources/mp4s/portal_data_download.mp4\" autoplay muted loop controls style=\"width:100%\"></p>\n",
Expand All @@ -144,7 +144,7 @@
"import os # for paths and mkdir\n",
"\n",
"# dataset name is the folder name for your dataset\n",
"datasetName = 'ellipsoid-v1'\n",
"datasetName = 'ellipsoid_1mode'\n",
"\n",
"# path to the dataset where we can find shape data \n",
"# here we assume shape data are given as surface meshes\n",
Expand Down
4 changes: 2 additions & 2 deletions Examples/Python/notebooks/tutorials/getting-started-with-segmentations.ipynb
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Expand Up @@ -130,7 +130,7 @@
"After you login, click `Collections` on the left panel and then `use-case-data-v2`. Select the dataset you would like to download by clicking on the checkbox on the left of the dataset name. See the video below.\n",
"After you download the dataset zip file, make sure you unzip/extract the contents in the appropriate location.\n",
"\n",
"**This notebook assumes that you have downloaded `ellipsoid-v1` and you have placed the unzipped folder `ellipsoid-v1` in `Examples/Python/Data`.** Feel free to use your own dataset. \n",
"**This notebook assumes that you have downloaded `ellipsoid_1mode` and you have placed the unzipped folder `ellipsoid_1mode` in `Examples/Python/Data`.** Feel free to use your own dataset. \n",
"\n",
"\n",
"<p><video src=\"https://sci.utah.edu/~shapeworks/doc-resources/mp4s/portal_data_download.mp4\" autoplay muted loop controls style=\"width:100%\"></p>\n"
Expand All @@ -145,7 +145,7 @@
"import os # for paths and mkdir\n",
"\n",
"# dataset name is the folder name for your dataset\n",
"datasetName = 'ellipsoid-v1'\n",
"datasetName = 'ellipsoid_1mode'\n",
"\n",
"# path to the dataset where we can find shape data \n",
"# here we assume shape data are given as binary segmentations\n",
Expand Down
16 changes: 15 additions & 1 deletion Examples/Python/notebooks/tutorials/getting-started-with-shape-cohort-generation.ipynb
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Expand Up @@ -540,7 +540,20 @@
" Datatype : `bool` <br> \n",
" Defaut value : `True` <br>\n",
" <br> \n",
"- `randomize_rotation`: randomizes the orientation of the ellispoids if set to `True` <br>\n",
"- `randomize_rotation`: randomizes the orientation of the ellipsoid if set to `True` <br>\n",
" Datatype : `bool` <br> \n",
" Defaut value : `True`\n",
" <br>\n",
" \n",
"- `randomize_x_radius`: randomizes the radius of the ellipsoid along x-axis if set to `True` or else the value is fixed as 20 for all ellipsoids<br>\n",
" Datatype : `bool` <br> \n",
" Defaut value : `True`\n",
" <br>\n",
"- `randomize_y_radius`: randomizes the radius of the ellipsoid along y-axis if set to `True` or else the value is fixed as 10 for all ellipsoids<br>\n",
" Datatype : `bool` <br> \n",
" Defaut value : `True`\n",
" <br>\n",
"- `randomize_z_radius`: randomizes the radius of the ellipsoid along z-axis if set to `True` or else the value is fixed as 10 for all ellipsoids<br>\n",
" Datatype : `bool` <br> \n",
" Defaut value : `True`\n",
" <br>"
Expand Down Expand Up @@ -610,6 +623,7 @@
" Datatype : `bool` <br> \n",
" Defaut value : `True`\n",
" <br>\n",
" \n",
"- `spacing`: set the spacing of the segmentation image <br>\n",
" Datatype: `list` <br>\n",
" Default value: `[1,1,1]` <br>\n",
Expand Down
4 changes: 2 additions & 2 deletions Python/ShapeCohortGenPackage/ShapeCohortGen/CohortGenerator.py
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Expand Up @@ -22,8 +22,8 @@ def generate_images(self, blur_factor=1, foreground_mean=180, foreground_var=30,
class EllipsoidCohortGenerator(CohortGenerator):
def __init__(self,out_dir):
super().__init__(out_dir)
def generate(self, num_samples=3, randomize_center=True, randomize_rotation=True):
self.meshes = Ellipsoids.generate(num_samples, self.out_dir, randomize_center, randomize_rotation)
def generate(self, num_samples=3, randomize_center=True, randomize_rotation=True, randomize_x_radius=True, randomize_y_radius=True, randomize_z_radius=True):
self.meshes = Ellipsoids.generate(num_samples, self.out_dir, randomize_center, randomize_rotation, randomize_x_radius, randomize_y_radius, randomize_z_radius)
return self.meshes

class SupershapesCohortGenerator(CohortGenerator):
Expand Down
24 changes: 16 additions & 8 deletions Python/ShapeCohortGenPackage/ShapeCohortGen/Ellipsoids.py
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Expand Up @@ -35,18 +35,26 @@ def addEllipsoid(center, radii, rotation, resolution=24):

return translateFilter

def generate_ellipsoids(filename, meshDir, randomize_center, randomize_rotation):
def generate_ellipsoids(filename, meshDir, randomize_center, randomize_rotation, randomize_x_radius, randomize_y_radius, randomize_z_radius):
vtkFileName = meshDir+"ellipsoid_"+filename+".vtk"
plyFileName = meshDir+"ellipsoid_"+filename+".ply"
if randomize_center:
center_loc = list(np.random.randint(low = 0,high=50,size=3))
else:
center_loc = [0,0,0]
x_radius = np.random.randint(low =15,high=25,size =1)
y_radius = np.random.randint(low =5,high=15,size =1)
z_radius = np.random.randint(low =5,high=15,size =1)

radii = [x_radius[0],y_radius[0],z_radius[0]]
if randomize_x_radius:
x_radius = np.random.randint(low =15,high=25,size =1)[0]
else:
x_radius = 20
if randomize_y_radius:
y_radius = np.random.randint(low =5,high=15,size =1)[0]
else:
y_radius = 10
if randomize_z_radius:
z_radius = np.random.randint(low =5,high=15,size =1)[0]
else:
z_radius = 12
radii = [x_radius,y_radius,z_radius]
if randomize_rotation:
rotation = np.random.randint(low=0,high=180,size=1)[0]
else:
Expand All @@ -64,10 +72,10 @@ def generate_ellipsoids(filename, meshDir, randomize_center, randomize_rotation)
vtk_writer.Update()


def generate(num_samples,out_dir,randomize_center, randomize_rotation):
def generate(num_samples,out_dir,randomize_center, randomize_rotation, randomize_x_radius, randomize_y_radius, randomize_z_radius):
meshDir = out_dir + "meshes/"
make_dir(meshDir)
for i in range(num_samples):
filename = str(i).zfill(2)
generate_ellipsoids(filename, meshDir, randomize_center, randomize_rotation)
generate_ellipsoids(filename, meshDir, randomize_center, randomize_rotation, randomize_x_radius, randomize_y_radius, randomize_z_radius)
return get_files(meshDir)
16 changes: 15 additions & 1 deletion docs/notebooks/getting-started-with-shape-cohort-generation.ipynb
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Expand Up @@ -540,7 +540,20 @@
" Datatype : `bool` <br> \n",
" Defaut value : `True` <br>\n",
" <br> \n",
"- `randomize_rotation`: randomizes the orientation of the ellispoids if set to `True` <br>\n",
"- `randomize_rotation`: randomizes the orientation of the ellipsoid if set to `True` <br>\n",
" Datatype : `bool` <br> \n",
" Defaut value : `True`\n",
" <br>\n",
" \n",
"- `randomize_x_radius`: randomizes the radius of the ellipsoid along x-axis if set to `True` or else the value is fixed as 20 for all ellipsoids<br>\n",
" Datatype : `bool` <br> \n",
" Defaut value : `True`\n",
" <br>\n",
"- `randomize_y_radius`: randomizes the radius of the ellipsoid along y-axis if set to `True` or else the value is fixed as 10 for all ellipsoids<br>\n",
" Datatype : `bool` <br> \n",
" Defaut value : `True`\n",
" <br>\n",
"- `randomize_z_radius`: randomizes the radius of the ellipsoid along z-axis if set to `True` or else the value is fixed as 10 for all ellipsoids<br>\n",
" Datatype : `bool` <br> \n",
" Defaut value : `True`\n",
" <br>"
Expand Down Expand Up @@ -610,6 +623,7 @@
" Datatype : `bool` <br> \n",
" Defaut value : `True`\n",
" <br>\n",
" \n",
"- `spacing`: set the spacing of the segmentation image <br>\n",
" Datatype: `list` <br>\n",
" Default value: `[1,1,1]` <br>\n",
Expand Down