Reconstruction

tomopy-ij

To reconstruct using the tomopy ij:

[tomo@handyn]$ bash
[tomo@handyn]$ activate tomopy-cli

start Fiji:

(tomopy-cli) tomo@handyn ~ $ /home/beams/TOMO/Software/Fiji.app/ImageJ-linux64

then ImageJ->File->Open and select /local/tomo/conda/tomopy-ij/tomopy_ij.py:

imagej-ij

then press run on:

imagej-ij-run

to obtain the main tomopy-ij screen:

imagej-ij-start

for more details check tomopy ij.

tomopy-cli

To manually reconstruct a data set, use the tomopy cli:

[tomo@handyn]$ tomopy recon --file-name /local/data/YYYY-MM/PI_lastName/file.h5

To automatically find the center for all data sets in a directory use:

[tomo@handyn]$ tomopy find_center --file-name /local/data/2021-02/Stock/180/

this command will generate a parameter file (extra_params.yaml) containing the centers.

To run a single slice reconstruction on all the data sets using the parameter file use:

[tomo@handyn]$ tomopy recon  --rotation-axis-auto manual  --gridrec-padding True --nsino 0.5 --reconstruction-type slice --file-name  /local/data/2021-02/Stock/180/ --parameter-file /local/data/2021-02/Stock/180/extra_params.yaml

After inspecting the reconstructed slices, you can adjust the center by editing the parameter file, then you can run the full reconstruction for all data sets with:

[tomo@handyn]$ tomopy recon  --gridrec-padding True --remove-stripe-method fw --fw-pad True --nsino-per-chunk 128 --reconstruction-type full --file-name  /local/data/2021-02/Stock/180/ --parameter-file /local/data/2021-02/Stock/180/extra_params.yaml

360 deg data sets

To do a try reconstrution on a 0-360 deg data set run:

[tomo@handyn]$ tomopy recon --reconstruction-type try --rotation-axis-auto manual --gridrec-padding True --remove-stripe-method fw --fw-pad True  --file-type double_fov --rotation-axis 50 --center-search-width 45 --file-name /local/data/2021-02/Stock/360/01_010.h5

once the center is selected run the full reconstruction with:

[tomo@handyn]$ tomopy recon --reconstruction-type full --rotation-axis-auto manual --gridrec-padding True --remove-stripe-method fw --fw-pad True  --nsino-per-chunk 128 --file-type double_fov   --file-name /local/data/2021-02/Stock/360/01_010.h5 --rotation-axis 30.0