add bad_bpms_summary (#427)

* add bad_bpms_summary
* doc, version
* test
---------

Co-authored-by: JoschD <[email protected]>

Author: awegsche

.zenodo.json

@@ -5,57 +5,66 @@
             "affiliation": "CERN"
         },
         {
-            "name": "Lukáš Malina",
+            "name": "Felix Simon Carlier",
             "affiliation": "CERN",
-            "orcid": "0000-0002-4673-6035"
+            "orcid": "0000-0002-7173-8833"
         },
         {
-            "name": "Joschua Dilly",
+            "name": "Jaime Maria Coello De Portugal - Martinez Vazquez",
             "affiliation": "CERN",
-            "orcid": "0000-0001-7864-5448"
+            "orcid": "0000-0002-6899-3809"
         },
         {
-            "name": "Michael Hofer",
+            "name": "Joschua Dilly",
             "affiliation": "CERN",
-            "orcid": "0000-0001-6173-0232"
-        },
-        {
-            "name": "Felix Soubelet",
-            "affiliation": "University of Liverpool & CERN",
-            "orcid": "0000-0001-8012-1440"
-        },
-        {
-            "name": "Andreas Wegscheider",
-            "affiliation": "CERN"
+            "orcid": "0000-0001-7864-5448"
         },
         {
-            "name": "Jaime Maria Coello De Portugal - Martinez Vazquez",
+            "name": "Hector Garcia Morales",
             "affiliation": "CERN",
-            "orcid": "0000-0002-6899-3809"
+            "orcid": "0000-0001-5100-8975"
         },
         {
             "name": "Maël Le Garrec",
             "affiliation": "CERN",
             "orcid": "0000-0002-8146-2340"
         },
         {
-            "name": "Tobias Persson",
+            "name": "Joshua Mark Gray",
             "affiliation": "CERN"
         },
+        {
+            "name": "Michael Hofer",
+            "affiliation": "CERN",
+            "orcid": "0000-0001-6173-0232"
+        },
         {
             "name": "Jacqueline Keintzel",
             "affiliation": "CERN",
             "orcid": "0000-0003-1396-8478"
         },
         {
-            "name": "Hector Garcia Morales",
+            "name": "Lukáš Malina",
             "affiliation": "CERN",
-            "orcid": "0000-0001-5100-8975"
+            "orcid": "0000-0002-4673-6035"
+        },
+        {
+            "name": "Tobias Persson",
+            "affiliation": "CERN"
+        },
+        {
+            "name": "Felix Soubelet",
+            "affiliation": "University of Liverpool & CERN",
+            "orcid": "0000-0001-8012-1440"
         },
         {
             "name": "Rogelio Tomas Garcia",
             "affiliation": "CERN",
             "orcid": "0000-0002-9857-1703"
+        },
+        {
+            "name": "Andreas Wegscheider",
+            "affiliation": "CERN"
         }
     ],
     "title": "OMC3",

CHANGELOG.md

@@ -1,5 +1,10 @@
 # OMC3 Changelog
 
+#### 2024-11-14 - v0.20.0 - _jdilly_, _awegsche_
+
+- Added:
+  - `bad_bpms_summary` script: Collect and summarize the bad BPMs from GUI runs.
+
 #### 2024-11-13 - v0.19.0 - _fscarlier_, _jdilly_
 
 - Added K-Modulation tools:

README.md

@@ -72,6 +72,7 @@ Other general utility scripts are in [`/omc3/scripts`](omc3/scripts):
 - `kmod_average.py` to calculate the average of multiple K-modulation measurements.
 - `kmod_import.py` to import a K-modulation measurement into an optics-measurement directory.
 - `kmod_lumi_imbalace.py` to calculate the luminosity imbalance between two IPs from averaged K-modulation files.
+- `bad_bpms_summary.py` to collect and summarize the bad BPMs from GUI runs.
 
 Example use for these scripts can be found in the [`tests`](tests) files.
 Documentation including relevant flags and parameters can be found at <https://pylhc.github.io/omc3/>.

doc/entrypoints/scripts.rst

@@ -40,3 +40,7 @@ Scripts
     :members:
     :noindex:
 
+
+.. automodule:: omc3.scripts.bad_bpms_summary
+    :members:
+    :noindex:

omc3/__init__.py

@@ -11,7 +11,7 @@
 __title__ = "omc3"
 __description__ = "An accelerator physics tools package for the OMC team at CERN."
 __url__ = "https://github.com/pylhc/omc3"
-__version__ = "0.19.0"
+__version__ = "0.20.0"
 __author__ = "pylhc"
 __author_email__ = "[email protected]"
 __license__ = "MIT"

omc3/optics_measurements/iforest.py

@@ -5,9 +5,11 @@
 This module contains the isolation forest functionality of ``optics_measurements``.
 It provides functions to detect and exclude BPMs with anomalies.
 """
+from pathlib import Path
 import numpy as np
 import pandas as pd
 from sklearn.ensemble import IsolationForest
+import tfs
 
 from omc3.definitions.constants import PLANE_TO_NUM
 from omc3.utils import logging_tools
@@ -21,8 +23,8 @@ def clean_with_isolation_forest(input_files, meas_input, plane):
     bad_bpms = identify_bad_bpms(meas_input, input_files, plane)
     input_files = remove_bad_bpms(input_files, list(set(bad_bpms.NAME)), plane)
     LOGGER.info(str(list(set(bad_bpms.NAME))))
-    # TODO potentially write output files ... currently not unique indices!
-    #  tfs.write(os.path.join(meas_input.outputdir, f"bad_bpms_iforest_{plane.lower()}.tfs"), bad_bpms)
+    if meas_input.outputdir is not None:
+        tfs.write(Path(meas_input.outputdir)/ f"bad_bpms_iforest_{plane.lower()}.tfs", bad_bpms)
     return input_files