CRTC I2M - Revision history

Spyridon97 at 23:37, 23 July 2020

2020-07-23T23:37:26Z

Spyridon97 at 23:33, 23 July 2020

2020-07-23T23:33:46Z

Spyridon97 at 22:43, 23 July 2020

2020-07-23T22:43:42Z

Spyridon97 at 22:36, 23 July 2020

2020-07-23T22:36:33Z

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Spyridon97 at 21:24, 23 July 2020

2020-07-23T21:24:44Z

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Spyridon97 at 21:06, 23 July 2020

2020-07-23T21:06:43Z

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Spyridon97 at 21:00, 23 July 2020

2020-07-23T21:00:44Z

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Nikos: /* Computataional Biology */

2020-06-22T18:44:56Z

‎Computataional Biology

Nikos: /* Problem Domains */

2020-06-22T18:39:30Z

‎Problem Domains

Spyridon97: /* Partons To NRRD */

2020-06-02T20:02:28Z

‎Partons To NRRD

← Older revision		Revision as of 23:37, 23 July 2020
Line 386:		Line 386:


−	The input image is used as a background(BG) mesh while refining the mesh. Before the beginning of the refinement, the input image is analyzed, and the ''image-weight-range'' along with the diagonal of the image are computed, The diagonal is used to define the ''minimum-element-edge-length'' and ''maximum-element-edge-length'' multiplied by the user-defined ''min-edge'' and ''max-edge'' diagonal percentages. The refinement algorithm queries the sizing function (SF) to verify whether each element satisfies the user constrains. Each time SF is called upon an element, it will check if it meets the size constrains ''minimum-element-edge-length'' and ''maximum-element-edge-size''. Consequently, it will create a set SP of sampling points out of the element. This set consists of the element’s vertices, barycenter, and midpoints of vertices and barycenter. The sampling points that are preserved out of SP are those that lie within the BG mesh. Using the BG mesh, a set V of the values of SP is created. Subsequently, the ''element-weight-range'' = abs(max(V) - min(V)) is evaluated. If ''element-weight-range''/''image-weight-range'' exceeds the user constraint ''weight-limit'', the element is split.	+	The input image is used as a background(BG) mesh while refining the mesh. Before the beginning of the refinement, the input image is analyzed, and the ''image-weight-range'' along with the diagonal of the image are computed, The diagonal is used to define the ''minimum-element-edge-length'' and ''maximum-element-edge-length'' multiplied by the user-defined ''min-edge'' and ''max-edge'' diagonal percentages. The refinement algorithm queries the sizing function (SF) to verify whether each element satisfies the user constrains. Each time SF is called upon an element, it will check if it meets the size constrains ''minimum-element-edge-length'' and ''maximum-element-edge-size''. Consequently, it will create a set SP of sampling points out of the element. This set consists of the element’s vertices, barycenter, and midpoints of vertices and barycenter. The sampling points that are preserved out of SP are those that lie within the BG mesh. Using the BG mesh, a set V of the values of SP is created. Subsequently, the ''element-weight-range'' = abs(max(V) - min(V)) is evaluated. If ''element-weight-range'' / ''image-weight-range'' exceeds the user constraint ''weight-limit'', the element is split.

	The described sizing function was designed for the Computational Nuclear Femtography data. Nonetheless, another sizing function could be designed and employed if requested.		The described sizing function was designed for the Computational Nuclear Femtography data. Nonetheless, another sizing function could be designed and employed if requested.

← Older revision		Revision as of 23:33, 23 July 2020
Line 386:		Line 386:


−	The input image is used as a background(BG) mesh while refining the mesh. Before the beginning of the refinement, the input image is analyzed, and the ''image-weight-range'' along with the diagonal of the image are computed, The diagonal is used to define the ''minimum-element-edge-length'' and ''maximum-element-edge-length'' multiplied by ~~the~~ the user-defined ''min-edge'' and ''max-edge'' diagonal percentages. The refinement algorithm queries the sizing function (SF) to verify whether each element satisfies the user constrains. Each time SF is called upon an element, it will check if it meets the size constrains ''minimum-element-edge-length'' and ''maximum-element-edge-size''. Consequently, it will create a set SP of sampling points out of the element. This set consists of the element’s vertices, barycenter, and midpoints of vertices and barycenter. The sampling points that are preserved out of SP are those that lie within the BG mesh. Using the BG mesh, a set V of the values of SP is created. Subsequently, the ''element-weight-range'' = abs(max(V) - min(V)) is evaluated. If ''element-weight-range''/''image-weight-range'' exceeds the user constraint ''weight-limit'', the element is split.	+	The input image is used as a background(BG) mesh while refining the mesh. Before the beginning of the refinement, the input image is analyzed, and the ''image-weight-range'' along with the diagonal of the image are computed, The diagonal is used to define the ''minimum-element-edge-length'' and ''maximum-element-edge-length'' multiplied by the user-defined ''min-edge'' and ''max-edge'' diagonal percentages. The refinement algorithm queries the sizing function (SF) to verify whether each element satisfies the user constrains. Each time SF is called upon an element, it will check if it meets the size constrains ''minimum-element-edge-length'' and ''maximum-element-edge-size''. Consequently, it will create a set SP of sampling points out of the element. This set consists of the element’s vertices, barycenter, and midpoints of vertices and barycenter. The sampling points that are preserved out of SP are those that lie within the BG mesh. Using the BG mesh, a set V of the values of SP is created. Subsequently, the ''element-weight-range'' = abs(max(V) - min(V)) is evaluated. If ''element-weight-range''/''image-weight-range'' exceeds the user constraint ''weight-limit'', the element is split.

	The described sizing function was designed for the Computational Nuclear Femtography data. Nonetheless, another sizing function could be designed and employed if requested.		The described sizing function was designed for the Computational Nuclear Femtography data. Nonetheless, another sizing function could be designed and employed if requested.

@@ Line 321: / Line 321: @@
 Constrains the amount of memory in MB that will be used.<br />
 (Default: 80% of the free memory).
 === Geometry Parameters ===
@@ Line 436: / Line 440: @@
 Below is the detailed information about the parameters of <code>tessellate2d</code>:
 <code>-i, --input [filename]</code> (required)
@@ Line 487: / Line 490: @@
 Controls the level of output text verbosity. <code>0</code> produces no output, and <code>1</code> produces standard output.<br />
 (Default: 1).
 == Convert Image ==

← Older revision		Revision as of 18:44, 22 June 2020
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	== Computataional Biology ==		== Computataional Biology ==
		+
		+	=3D Example Meshes=
		+	The directory containing the 3D input data is located in the 3D folder of [https://odu.box.com/s/9scj74ix4eulpvgc93sbwte1uvlde8b6 Bioninformatics_Data].
		+
		+	==COVID-19-Main-Protease-6y2e==
		+	* [https://odu.box.com/s/eb9s3vrvml0gop7mdpwckh6xnn27eiut Input Image]
		+	* Input image : Dimensions (284x303x344) with spacing (0.2226907x0.2226907x0.2226907)
		+	* Uniform with Delta = 0.3: 2,509,202 tetrahedra
		+
		+	<gallery mode="packed" heights=250px>
		+	File:COVID-19-Main-Protease-6y2e,d=0.5.png
		+	File:COVID-19-Main-Protease-6y2e,d=0.5,clip.png
		+	</gallery>
		+	<gallery mode="packed" heights=250px>
		+	File:COVID-19-Main-Protease-6y2e,d=0.5,label=1.png
		+	File:COVID-19-Main-Protease-6y2e,d=0.5,label=2.png
		+	</gallery>
		+
		+	Commands to generate meshes:
		+
		+	'''Uniform with Delta = 0.3:''' [https://odu.box.com/s/jeks38sn5slw38gbit6t0rf25fzv6jpb Output Mesh]
		+	<pre>
		+	docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/COVID-19-Main-Protease-6y2e.nrrd --delta 0.3 --output ./COVID-19-Main-Protease-6y2e,d=0.3.vtk
		+	</pre>
		+
		+	Uniform tetrahedral mesh capable to help identify the internal voids of the <b>COVID-19 Main Protease. </b> Biological assembly data was retrieved from the molecule [https://www.rcsb.org/structure/6y2e 6y2e], [https://www.rcsb.org/ Protein Data Bank].
		+
		+	==COVID-19-NSP-15-Endoribonuclease-6vww==
		+	* [Input Image]
		+	* Input image : Dimensions (303x297x337) with spacing (0.3445713x0.3445713x0.3445713)
		+	* Uniform with Delta = 0.5: 2,310,215 tetrahedra
		+
		+	<gallery mode="packed" heights=250px>
		+	File:COVID-19-NSP-15-Endoribonuclease-6vww,d=0.3.png
		+	File:COVID-19-NSP-15-Endoribonuclease-6vww,d=0.3,clip.png
		+	</gallery>
		+	<gallery mode="packed" heights=250px>
		+	File:COVID-19-NSP-15-Endoribonuclease-6vww,d=0.3,label=1.png
		+	File:COVID-19-NSP-15-Endoribonuclease-6vww,d=0.3,label=2.png
		+	File:COVID-19-NSP-15-Endoribonuclease-6vww,d=0.3,label=3.png
		+	</gallery>
		+
		+	Commands to generate meshes:
		+
		+	'''Uniform with Delta = 0.5:''' [https://odu.box.com/s/tkk8f8o1tctf52bop07a6hxy87ugt8kg Output Mesh]
		+	<pre>
		+	docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/COVID-19-NSP-15-Endoribonuclease-6vww.nrrd --delta 0.5 --output ./COVID-19-NSP-15-Endoribonuclease-6vww,d=0.5.vtk
		+	</pre>
		+
		+	Uniform tetrahedral mesh capable to help identify the internal voids of the <b>COVID-19 NSP15 Endoribonuclease. </b> Biological assembly data was retrieved from the molecule [https://www.rcsb.org/structure/6vww 6vww], [https://www.rcsb.org/ Protein Data Bank].
		+
		+	==COVID-19-Spike-Glycoprotein-6vxx==
		+	* [https://odu.box.com/s/jt2z4vqq3vs8211uuah7m2qfnyk1tjq8 Input Image]
		+	* Input image : Dimensions (281x380x302) with spacing (0.427871x0.427871x0.427871)
		+	* Uniform with Delta = 0.5: 3,260,055 tetrahedra
		+
		+	<gallery mode="packed" heights=250px>
		+	File:COVID-19-Spike-Glycoprotein-6vxx,d=5.png
		+	File:COVID-19-Spike-Glycoprotein-6vxx,d=5,zoom.png
		+	</gallery>
		+
		+	<gallery mode="packed" heights=250px>
		+	File:COVID-19-Spike-Glycoprotein-6vxx,d=5,label=1.png
		+	File:COVID-19-Spike-Glycoprotein-6vxx,d=5,label=2.png
		+	File:COVID-19-Spike-Glycoprotein-6vxx,d=5,label=3.png
		+	</gallery>
		+
		+	Commands to generate meshes:
		+
		+	'''Uniform with Delta = 0.5:''' [https://odu.box.com/s/0s3zxk3t2hsvmt43l4i9pabm602tiqbk Output Mesh]
		+	<pre>
		+	docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/COVID-19-Spike-Glycoprotein-6vxx.nrrd --delta 0.5 --output ./COVID-19-Spike-Glycoprotein-6vxx,d=5.vtk
		+	</pre>
		+
		+	Uniform tetrahedral mesh capable to help identify the internal voids of the <b>COVID-19 spike glycoprotein. </b> Biological assembly data was retrieved from the molecule [https://www.rcsb.org/structure/6vxx 6vxx], [https://www.rcsb.org/ Protein Data Bank].
		+
		+	==COVID-19-Spike-Glycoprotein-6vsb==
		+	* [https://odu.box.com/s/hebeasclyuekcavgvftb9vbsirrbqj7t Input Image]
		+	* Input image : Dimensions (220x223x314) with spacing (0.551042x0.551042x0.551042)
		+	* Uniform with Delta = 0.4: 5,731,833 tetrahedra
		+	* Graded with Delta = 0.4: 3,794,223 tetrahedra
		+
		+	<gallery mode="packed" heights=250px>
		+	File:COVID-19-Spike-Glycoprotein-6vsb,d=0.4.png
		+	File:COVID-19-Spike-Glycoprotein-6vsb,d=0.4,clip.png
		+	</gallery>
		+	<gallery mode="packed" heights=250px>
		+	File:COVID-19-Spike-Glycoprotein-6vsb,d=0.4,graded.png
		+	File:COVID-19-Spike-Glycoprotein-6vsb,d=0.4,graded,clip.png
		+	</gallery>
		+
		+	Commands to generate meshes:
		+
		+	'''Uniform with Delta = 0.4:''' [https://odu.box.com/s/wth64bzfotibrwv3t25kn2oyzo0dqntm Output Mesh]
		+	<pre>
		+	docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/COVID-19-Spike-Glycoprotein-6vsb.nrrd --delta 0.4 --output ./COVID-19-Spike-Glycoprotein-6vsb,d=0.4.vtk
		+	</pre>
		+
		+	'''Graded with Delta = 0.4:''' [https://odu.box.com/s/2kn1ovwpa6jarj8wssmeqz2y5zc19fc2 Output Mesh]
		+	<pre>
		+	docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/COVID-19-Spike-Glycoprotein-6vsb.nrrd --delta 0.4 --volume-grading --output ./COVID-19-Spike-Glycoprotein-6vsb,d=0.4,graded.vtk
		+	</pre>
		+
		+	Uniform and graded tetrahedral meshes capable to help identify the internal voids of the <b>COVID-19 spike glycoprotein. </b> The middle and right meshes are slices. Biological assembly data was retrieved from the molecule [https://www.rcsb.org/structure/6vxx 6vxx], [https://www.rcsb.org/ Protein Data Bank].
		+

	=== Tessellate2D ===		=== Tessellate2D ===

← Older revision		Revision as of 18:39, 22 June 2020
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	Labels that will be excluded from the mesh. Keeps all labels in the mesh except the ones specified. If not specified, all labels will be included in the mesh. Cannot be used together with <code>--include-labels</code>.		Labels that will be excluded from the mesh. Keeps all labels in the mesh except the ones specified. If not specified, all labels will be included in the mesh. Cannot be used together with <code>--include-labels</code>.
		+
		+	== Computataional Biology ==

	=== Tessellate2D ===		=== Tessellate2D ===

@@ Line 522: / Line 522: @@
 == Partons To NRRD ==
-<code>partonsToNRRD</code> serves as a utility to create images out of partons data
+<code>partonsToNRRD</code> serves as a utility to create images out of partons data.
 <pre>docker run -v $(pwd):/data/ crtc_i2m partonsToNRRD partonsFile.dat columnId xBins yBins zBins</pre>
 = Appendix =