Update post_processing.md

cleaned up psf post proc

docs/source/post_processing.md

@@ -10,59 +10,7 @@ catalogue via _metacalibration_), a joint star catalogue, and PSF diagnostic plo
 If main ShapePipe processing happened at the old canfar VM system (e.g. CFIS v0 and v1), go
 [here](vos_retrieve.md) for details how to retrieve the ShapePipe output files.
 
-Some of the following steps pertain specifically to runs carried out on [canfar](https://www.canfar.net/en),
-but most are general.
-
-1. Retrieve `ShapePipe` result files
-
-   For a local run on the same machine as for post-processing, nothing needs to be done.
-   In some cases, the run was carried out on a remote machine or cluster, and the resulting `ShapePipe`
-   output files need to be retrieved.
-
-   In the specific case of canfar_avail_results.py, this is done as follows.
-
-   A. Check availability of results
-
-      A `canfar` job can submit a large number of tiles, whose processing time can vary a lot.
-      We assume that the submitted tile ID list is available locally via the ascii file `tile_numbers.txt`. 
-      To check which tiles have finished running, and whose results have been uploaded, use
-      ```bash
-      canfar_avail_results -i tile_numbers.txt -v -p PSF --input_path INPUT_PATH
-      ```
-      where PSF is one in [`psfex`|`mccd`], and INPUT_PATH the input path on vos, default `vos:cfis/cosmostat/kilbinger/results`.
-      See `-h` for all options.
-
-   B. Download results
-
-      All results files will be downloaded with
-      ```bash
-      canfar_download_results -i tile_numbers.txt -v -p PSF --input_vos INPUT_VOS
-      ```
-      Use the same options as for same as for `canfar_avail_results`.
-
-      This command can be run in the same directory at subsequent times, to complete an ongoing run: Only newer files will be downloaded
-      from the `vos` directory. This also assures that partially downloaded or corrupt files will be replaced.
-
-      Checking the `vos` directorty can be slow for large patches.
-      To only download files that are not yet present locally (in `.`), first write the missing ones to an ascii file, using again the
-      script `canfar_avail_results`, but this time with `.` as input path:
-      ```bash
-      canfar_avail_results -i tile_numbers.txt --input_path . -p PSF -v -o missing.txt
-      '''
-      Then, download only the missing files with
-      ```bash
-      canfar_download_results -i missing.txt --input_vos cosmostat/kilbinger/results_mccd_oc2 -p mccd -v
-      ```
-
-   C. Un-tar results
-     ```bash
-      untar_results -p PSF
-      ```
-      On success, `ShapePipe` output `fits` and `log` files will be now in various subdirs of the `output` directory.
-
-At this step all required `ShapePipe` resulting output files are available in the current working directory.
-
-2. Optional: Split output in sub-samples
+1. Optional: Split output into sub-samples
 
    An optional intermediate step is to create directories for sub-samples, for example one directory
    for each patch on the sky. This will create symbolic links to the results `.tgz` files downloaded in
@@ -73,33 +21,34 @@ At this step all required `ShapePipe` resulting output files are available in th
     ```
     The following steps will then be done in the directory `tiles_W3`.
 
-3. Run PSF diagnostics, create merged catalogue
+2. Run PSF diagnostics, create merged catalogue
 
    Type
    ```bash
    post_proc_sp -p PSF
    ```
-   to automatically perform a number of post-processing steps. Chose the PSF model with the option
+   to automatically perform a number of post-processing steps. Choose the PSF model with the option
    `-p psfex|mccd`. In detail, these are (and can also be done individually
    by hand):
 
-   A. Analyse psf validation files
+   1. Analyse psf validation files
 
       ```bash
-      prepare_star_cat -p PSF
+      combine_runs -t psf -p PSF
       ```
       with options as for `post_proc_sp`.
-      This script identifies all psf validation files (from all processed tiles downloaded to `pwd`), creates symbolic links,
-      merges the catalogues, and creates plots of PSF ellipticity, size, and residuals over the focal plane.
+      This script creates a new combined psf run in the ShapePipe `output` directory, by identifying all psf validation files
+      and creating symbolic links. The run log file is updated.
 
-   B. Create plots of the PSF and their residuals in the focal plane, as a diagnostic of the overall PSF model.
-     As a scale-dependend test, which propagates directly to the shear correlation function, the rho statistics are computed,
-     see {cite:p}`rowe:10` and {cite:p}`jarvis:16`,
+   3. Merge individual psf validation files into one catalogue. Create plots of the PSF and their residuals in the focal plane,
+      as a diagnostic of the overall PSF model.
+      As a scale-dependend test, which propagates directly to the shear correlation function, the rho statistics are computed,
+      see {cite:p}`rowe:10` and {cite:p}`jarvis:16`,
       ```bash
       shapepipe_run -c /path/to/shapepipe/example/cfis/config_MsPl_PSF.ini
       ``` 
 
-   C. Prepare output directory
+   4. Prepare output directory
 
       Create links to all 'final_cat' result files with 
       ```bash
@@ -108,7 +57,7 @@ At this step all required `ShapePipe` resulting output files are available in th
       The corresponding output directory that is created is `output/run_sp_combined/make_catalog_runner/output`.
       On success, it contains links to all `final_cat` output catalogues
 
-   D. Merge final output files
+   5. Merge final output files
 
       Create a single main shape catalog:
       ```bash