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--- pipeline:isac:sxisac2 [2018/02/21 16:59]
moriya
+++ pipeline:isac:sxisac2 [2018/08/22 11:01]
fmerino
@@ Line 32: / Line 32: @@
 === Main Parameters ===
   ; stack_file : Input image stack: The images must to be square (//nx//=//ny//). The stack can be either in bdb or hdf format. (default required string)
-  ; output_directory : Output directory: The directory will be automatically created and the results will be written here. If the directory already exists, results will be written there, possibly overwriting previous runs. (default required string)
+  ; output_directory : Output directory: The automatically-created output directory will contain results. If the directory already exists, results will be written there, possibly overwriting previous runs. (default required string)
   ; %%--%%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//, where //N// is the total number of images in the input stack. (default 200)
   ; %%--%%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)
   ; %%--%%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, depends linearly on square of radius (parameter //ou//). //units// - //pixels//. (default 0.7)
   ; %%--%%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// + //xr// - 1  (default 76)
-\\
-=== 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)
   ; %%--%%rs : Ring step [Pixels]: Step of the resampling to polar coordinates. (default 1)
@@ Line 65: / Line 65: @@
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 ===== 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 (OBSOLETE?!!, it typically have 3~9 iterations of matching). The first half of iterations are 2-way matching, the second half of iterations are 3-way matching, and the last iteration is 4-way matching. In the second phase, three files will be generated:
+The second phase is where the actual class averages are generated. The candidate groups are tested for their stability by repeated randomly initialized reference-free alignment and those deemed stable as set aside as output and member images of those that did not pass the test are returned to the overall pool of data and processed again starting from the first phase.
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@@ Line 108: / Line 108: @@
 ==== Time and Memory ====
-Unfortunately, ISAC2 is very time- and memory-consuming. (OBSLETE?!! For example, on my cluster, it takes 15 hours to process 50,000 64x64 particles on 256 processors. Therefore, before embarking on the big dataset, it is recommended to run a test dataset (about 2,000~5,000 particles) first to get a rough idea of timing.)
+ISAC2 is very time- and memory-consuming.  For example, it may take 15 hours to process 50,000 particles using 256 processors. Therefore, before embarking on the big dataset, it is recommended to run a test dataset (about 20,000 particles) first to get a rough idea of timing.
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