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--- eman2:programfiles [2025/07/04 19:02] – created steveludtke
+++ eman2:programfiles [2026/03/25 14:24] (current) – steveludtke
@@ Line 88: / Line 88: @@
   * **classes_XX** - Class averages at the end of the iteration. The highest numbered classes_XX file is the final output of the program
+===== For the newer Single Particle Tomography Pipeline =====
+Most of the new pipeline commands will have a file in each folder (eg - spt_08/0_spt_params.json) named 0_something.json. These json files are just text files. If you cat them you will generally find out the information on how that folder was created. Similar command information is logged in .eman2log.txt (and .eman3log.txt for nascent EMAN3 pipelines).
-===== For Single Particle Tomography (SPT, "subtomogram averaging") =====
+==== e2spt_sgd_new.py ====
+Creates sptsgd_XX folders containing:
+  * 0_spt_params.json - details command options used when creating this folder (text file)
+  * output_all_clsX.hdf - will contain up to --niter volumes (fewer if you stopped it early) for class number X, there will be --ncls files. This is the entire evolution of that class during generation
+  * output_clsX.hdf - will always contain the last-generated volume for class X. There will be --ncls files.
+  * particle_info_2d.lst - a lst file with metadata about the 3-D alignment of each 2-D subtilt image, and information to relate to the 3-D particles
+  * particle_info_3d.lst - a lst file with metadata about the 3-D particles and links to the 2-D subtilts
+==== e2spt_refine_new.py ====
+creates spt_XX folders containing:
+  * 0_spt_params.json - details command options used when creating this folder (text file)
+  * mask.hdf - mask applied during refinement
+  * aliptcls2d_YY.lst - the aligned subtilt particles after each iteration (YY) with metadata. These can be used as inputs for further refinements or other programs
+  * aliptcls3d_YY.lst - the aligned 3D particles after each "P" iteration. Not generated for other iterations. Some programs will require 3D .lst files as inputs, and some will require 2D .lst files as inputs. The 3D alignments only change during "P" iterations, so you can combine a 2D .lst file from a later non-P iteration with the last-generated 3D file.
+  * threed_YY.hdf - The final output for iteration YY (masked/filtered)
+  * threed_YY_<even/odd>.hdf - filtered/masked even/odd maps for GSFSC in each iteration
+  * threed_YY_<even/odd>_unfilt.hdf - unfiltered/unmasked even/odd volumes after each iteration
+  * threed_YY_<even/odd>.txt - Only generated when using the EMAN3-style point based 3D reconstruction. These are the reconstructed points. Can be used with e3proctxt.py.
+===== For the older Single Particle Tomography (SPT, "subtomogram averaging") pipeline =====
 ==== Single stage alignment of subtomograms to a reference (e2spt_align.py) ====