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pipeline:isac:sxisac2 [2018/02/21 16:57] moriya |
pipeline:isac:sxisac2 [2018/08/22 11:01] fmerino |
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=== Main Parameters === | === Main Parameters === | ||
; stack_file : Input image stack: The images must to be square (// | ; stack_file : Input image stack: The images must to be square (// | ||
- | ; output_directory : Output directory: The directory will be automatically created and the results | + | ; output_directory : Output directory: The automatically-created output |
; %%--%%radius : Particle radius [Pixels]: Radius of the particle (pixels). There is no default value and so a sensible number has to be provided. (default required int) | ; %%--%%radius : Particle radius [Pixels]: Radius of the particle (pixels). There is no default value and so a sensible number has to be provided. (default required int) | ||
; %%--%%img_per_grp : Images per class: Number of images per class in an ideal situation. In practice, it defines the maximum size of the classes or the number of classes //K// = //N// / // | ; %%--%%img_per_grp : Images per class: Number of images per class in an ideal situation. In practice, it defines the maximum size of the classes or the number of classes //K// = //N// / // | ||
; %%--%%CTF : CTF phase flipping: If set, the data will be phase-flipped using CTF information included in the image headers. (default False) | ; %%--%%CTF : CTF phase flipping: If set, the data will be phase-flipped using CTF information included in the image headers. (default False) | ||
+ | ; %%--%%VPP : Phase Plate data: Please use this option if the dataset is taken with Phase Plate. (default False) | ||
+ | |||
+ | \\ | ||
+ | === Advanced Parameters === | ||
; %%--%%xr : Translation search range [Pixels]: The translational search range. Set by the program by default. (default 1) | ; %%--%%xr : Translation search range [Pixels]: The translational search range. Set by the program by default. (default 1) | ||
; %%--%%thld_err : Pixel error threshold [Pixels]: Used for checking stability. It is defined as the root mean square of distances between corresponding pixels from set of found transformations and theirs average transformation, | ; %%--%%thld_err : Pixel error threshold [Pixels]: Used for checking stability. It is defined as the root mean square of distances between corresponding pixels from set of found transformations and theirs average transformation, | ||
; %%--%%target_radius : Target particle radius [Pixels]: Particle radius used by ISAC2 to process the data. The images will be resized to fit this radius (default 29) | ; %%--%%target_radius : Target particle radius [Pixels]: Particle radius used by ISAC2 to process the data. The images will be resized to fit this radius (default 29) | ||
; %%--%%target_nx : Target particle image size [Pixels]: Image size used by ISAC2 to process the data. The images will be resized according to target particle radius and then cut/padded to achieve the target image size. When //xr// > 0, the final image size for ISAC2 processing is // | ; %%--%%target_nx : Target particle image size [Pixels]: Image size used by ISAC2 to process the data. The images will be resized according to target particle radius and then cut/padded to achieve the target image size. When //xr// > 0, the final image size for ISAC2 processing is // | ||
- | |||
- | \\ | ||
- | === Advanced Parameters === | ||
- | ; %%--%%VPP : Phase Plate data: Please use this option if the dataset is taken with Phase Plate. (default False) | ||
; %%--%%ir : Inner ring [Pixels]: Inner of the resampling to polar coordinates. (default 1) | ; %%--%%ir : Inner ring [Pixels]: Inner of the resampling to polar coordinates. (default 1) | ||
; %%--%%rs : Ring step [Pixels]: Step of the resampling to polar coordinates. (default 1) | ; %%--%%rs : Ring step [Pixels]: Step of the resampling to polar coordinates. (default 1) | ||
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===== Output ===== | ===== Output ===== | ||
- | For each generation of running the program, there are two phases. The first phase is an exploratory phase. In this phase, we set the criteria to be very loose and try to find as much candidate class averages as possible. (OBSOLETE? This phase typically should have 10 to 20 rounds). The candidate class averages are stored in class_averages_candidate_generation_n.hdf. | + | For each generation of running the program, there are two phases. The first phase is an exploratory phase. In this phase, we set the criteria to be very loose and try to find as much candidate class averages as possible. The candidate class averages are stored in class_averages_candidate_generation_n.hdf. |
- | The second phase is where the actual class averages are generated | + | The second phase is where the actual class averages are generated. The candidate groups |
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===== Description ===== | ===== Description ===== | ||
- | === Time and Memory === | ||
- | Unfortunately, ISAC2 is very time- and memory-consuming. | + | \\ |
+ | ==== 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 ==== | ||
+ | |||
+ | ISAC2 is very time- and memory-consuming. | ||
\\ | \\ | ||
- | === 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. | ||
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- |