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pipeline:isac:sxisac2 [2018/02/21 16:57] moriya |
pipeline:isac:sxisac2 [2018/02/21 16:58] moriya |
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===== Description ===== | ===== Description ===== | ||
- | === Time and Memory === | + | |
+ | \\ | ||
+ | ==== Method ==== | ||
+ | The program will perform the following steps (to save computation time, in case of inadvertent termination, | ||
+ | |||
+ | - The images in the input stacked will be phase-flipped. | ||
+ | - The data stack will be pre-aligned (output is in subdirectory 2dalignment, | ||
+ | * In case 2dalignment directory exists steps 1 and 2 are skipped. | ||
+ | - The alignment shift parameters will be applied to the input data. | ||
+ | - **IMPORTANT**: | ||
+ | * The pseudo-code for adjusting the size of the radius and the size of the images is as follows: | ||
+ | * shrink_ratio = target_radius / original_radius_size | ||
+ | * new_pixel_size = original_pixel_size * shrink_ratio | ||
+ | * if shrink_ratio is different than 1: resample images using shrink_ratio | ||
+ | * if new_pixel_size > target_nx : cut image to be target_nx in size | ||
+ | * if new_pixel_size < target_nx : pad image to be target_nx in size | ||
+ | * The target_radius and target_nx options allow the user to finely adjust the image so that it contains enough background information. | ||
+ | - The program will iterate through generations of ISAC2 by alternating two steps. The outcome of these two steps is in subdirectory generation_*** (stars replaced by the current generation number). | ||
+ | * Calculation of candidate class averages. | ||
+ | * Calculation of validated class averages. | ||
+ | - The program will terminate when it cannot find any more reproducible class averages. | ||
+ | - If no restart option is given the program will pick-up from the last saved point. | ||
+ | |||
+ | Also see the reference below. | ||
+ | |||
+ | ==== Time and Memory | ||
Unfortunately, | Unfortunately, | ||
\\ | \\ | ||
- | === Retrieval of images signed to selected group averages === | + | ==== Retrieval of images signed to selected group averages |
- Open in e2display.py file class_averages.hdf located in the main directory. | - Open in e2display.py file class_averages.hdf located in the main directory. | ||
- Delete averages whose member particles should not be included in the output. | - Delete averages whose member particles should not be included in the output. | ||
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- | === RCT information retrieval === | + | ==== RCT information retrieval |
Let us assume we would want to generate a RCT reconstruction using as a basis group number 12 from ISAC2 generation number 3. We have to do the following steps: | Let us assume we would want to generate a RCT reconstruction using as a basis group number 12 from ISAC2 generation number 3. We have to do the following steps: | ||
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- Extract the needed alignment parameters. | - Extract the needed alignment parameters. | ||
* $ sxheader.py | * $ sxheader.py | ||
- | |||
- | \\ | ||
- | ==== Method ==== | ||
- | The program will perform the following steps (to save computation time, in case of inadvertent termination, | ||
- | |||
- | - The images in the input stacked will be phase-flipped. | ||
- | - The data stack will be pre-aligned (output is in subdirectory 2dalignment, | ||
- | * In case 2dalignment directory exists steps 1 and 2 are skipped. | ||
- | - The alignment shift parameters will be applied to the input data. | ||
- | - **IMPORTANT**: | ||
- | * The pseudo-code for adjusting the size of the radius and the size of the images is as follows: | ||
- | * shrink_ratio = target_radius / original_radius_size | ||
- | * new_pixel_size = original_pixel_size * shrink_ratio | ||
- | * if shrink_ratio is different than 1: resample images using shrink_ratio | ||
- | * if new_pixel_size > target_nx : cut image to be target_nx in size | ||
- | * if new_pixel_size < target_nx : pad image to be target_nx in size | ||
- | * The target_radius and target_nx options allow the user to finely adjust the image so that it contains enough background information. | ||
- | - The program will iterate through generations of ISAC2 by alternating two steps. The outcome of these two steps is in subdirectory generation_*** (stars replaced by the current generation number). | ||
- | * Calculation of candidate class averages. | ||
- | * Calculation of validated class averages. | ||
- | - The program will terminate when it cannot find any more reproducible class averages. | ||
- | - If no restart option is given the program will pick-up from the last saved point. | ||
- | |||
- | Also see the reference below. | ||
\\ | \\ |