pipeline:isac:sxisac2
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pipeline:isac:sxisac2 [2018/02/21 16:57] moriya |
pipeline:isac:sxisac2 [2018/06/20 13:12] 127.0.0.1 external edit |
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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. | ||
| Line 97: | Line 123: | ||
| \\ | \\ | ||
| - | === 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: | ||
| Line 111: | Line 137: | ||
| - 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. | ||
| \\ | \\ | ||
pipeline/isac/sxisac2.txt · Last modified: 2020/08/19 16:40 by fschoenfeld
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