Merge pull request #64 from lsst-ts/issue/61/template_generator_phosim

Issue/61/template generator phosim

.gitignore

@@ -28,3 +28,6 @@ pytest_session.txt
 
 # Mac metadata
 .DS_Store
+
+# Existing Phosim Donut Templates
+policy/cwfs/donutTemplateData/phosimTemplates/

bin.src/runCreatePhosimDonutTemplates.py

@@ -0,0 +1,84 @@
+#!/usr/bin/env python
+
+# This file is part of ts_wep.
+#
+# Developed for the LSST Telescope and Site Systems.
+# This product includes software developed by the LSST Project
+# (https://www.lsst.org).
+# See the COPYRIGHT file at the top-level directory of this distribution
+# for details of code ownership.
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+import argparse
+
+from lsst.ts.wep.CreatePhosimDonutTemplates import CreatePhosimDonutTemplates
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser(
+        description="Generate donut templates for AOS using Phosim."
+    )
+    parser.add_argument(
+        "--numOfProc",
+        type=int,
+        default=1,
+        help="Number of processor to run PhoSim. (default: 1)",
+    )
+    parser.add_argument(
+        "--detectorList",
+        type=str,
+        default="",
+        help="""
+        Specify detectors.
+        By default will generate templates for all detectors.
+        (Example Input: "R22_S00 R22_S01 R22_S02")
+        """,
+    )
+    parser.add_argument(
+        "--templateSize",
+        type=int,
+        default=240,
+        help="Size of each side of the template in pixels. (default: 240)",
+    )
+    parser.add_argument(
+        "--intraVisitId",
+        type=int,
+        default=9006002,
+        help="Visit ID for phosim intrafocal images. (default: 9006002)",
+    )
+    parser.add_argument(
+        "--extraVisitId",
+        type=int,
+        default=9006001,
+        help="Visit ID for phosim extrafocal images. (default: 9006001)",
+    )
+    args = parser.parse_args()
+
+    # Run tasks
+    phosimDonuts = CreatePhosimDonutTemplates()
+    phosimDonuts.createWorkDirectories()
+    decListPhosim, decListFlats = phosimDonuts.createDetectorLists(
+        detectorStr=args.detectorList
+    )
+    phosimDonuts.generateDefocalImages(decListPhosim, args.numOfProc)
+    phosimDonuts.repackagePhosimImages()
+    phosimDonuts.ingestImages()
+    phosimDonuts.makeFlats(decListFlats)
+    phosimDonuts.ingestCalibs()
+    phosimDonuts.runISR()
+    phosimDonuts.cutOutIntraExtraTemplates(
+        args.templateSize, args.intraVisitId, args.extraVisitId
+    )
+    phosimDonuts.cleanUpWorkDirs()

doc/content.rst

@@ -32,6 +32,7 @@ This module is a high-level module to use other modules.
 * **PlotUtil**: Plot utility functions used in WEP.
 * **ParamReader**: Parameter reader class to read the yaml configuration files used in the calculation.
 * **DonutImageCheck**: Donut image check class to judge the donut image is effective or not.
+* **CreatePhosimDonutTemplates**: Create donut templates on camera detectors using Phosim. See :doc:`here <phosimDonutTemplates>` for more information on generating Phosim donut templates.
 
 .. _lsst.ts.wep-modules_wep_bsc:
 
@@ -109,6 +110,7 @@ This module calculates the wavefront error by solving the TIE.
 * **DonutTemplateFactory**: Factory for creating donut template objects used by CentroidConvolveTemplate.
 * **DonutTemplateDefault**: Default donut template class.
 * **DonutTemplateModel**: DonutTemplateDefault child class to make donut templates using an Instrument model.
+* **DonutTemplatePhosim**: DonutTemplateDefault child class to make donut templates from templates created with Phosim.
 
 .. _lsst.ts.wep-modules_wep_deblend:
 

doc/phosimDonutTemplates.rst

@@ -0,0 +1,32 @@
+.. py:currentmodule:: lsst.ts.wep
+
+.. _lsst.ts.wep-phosimDonutTemplates:
+
+########################################
+Creating Phosim Donut Templates
+########################################
+
+This document describes the code to generate the phosim donut templates
+that are used by :py:class:`DonutTemplatePhosim`.
+
+Running the code
+================
+
+1) Make sure your environment is set up to use ts_wep and that you have phosim
+   installed with the environment variable $PHOSIMPATH set to the phosim directory.
+2) Use python to run `runCreatePhosimDonutTemplates.py` in the bin.src directory.
+   Use `--help` to see all options.
+3) Templates will appear in
+   `ts_wep/policy/cwfs/templateDonutData/phosimTemplates`.
+
+Input files
+===========
+
+The following input files found in `policy/cwfs/donutTemplateData` are used
+to create the donut templates.
+
+* **starExtra.inst**: Phosim instance catalog to create one extra-focal donut per CCD
+                      of LSST camera using PhosimMapper.
+* **starIntra.inst**: Phosim instance catalog to create one intra-focal donut per CCD
+                      of LSST camera using PhosimMapper.
+* **star.cmd**: Phosim command file.

doc/uml/cwfsClass.uml

@@ -11,7 +11,9 @@ CentroidFindFactory ..> CentroidOtsu
 CentroidFindFactory ..> CentroidConvolveTemplate
 CentroidConvolveTemplate *-- CentroidRandomWalk
 DonutTemplateDefault <|-- DonutTemplateModel
+DonutTemplateDefault <|-- DonutTemplatePhosim
 DonutTemplateFactory ..> DonutTemplateModel
+DonutTemplateFactory ..> DonutTemplatePhosim
 DonutTemplateModel ..> CompensableImage
 DonutTemplateModel ..> Instrument
 Image ..> CentroidFindFactory

doc/uml/wepClass.uml

@@ -11,4 +11,6 @@ WepController ..> DefocalImage
 WepController ..> DonutImage
 SourceSelector *-- ParamReader
 SourceProcessor *-- ParamReader
+CreatePhosimDonutTemplates ..> CamIsrWrapper
+CreatePhosimDonutTemplates ..> CamDataCollector
 @enduml

doc/versionHistory.rst

@@ -6,13 +6,22 @@
 Version History
 ##################
 
+.. _lsst.ts.wep-1.5.3:
+
+-------------
+1.5.3
+-------------
+
+* Add ``DonutTemplatePhosim`` class.
+* Add ``CreatePhosimDonutTemplates`` class and add ``bin.src/runCreatePhosimDonutTemplates.py``
+
 .. _lsst.ts.wep-1.5.2:
 
 -------------
 1.5.2
 -------------
 
-* Fix the ``ZernikeMaskedFit()`` when passing masked data 
+* Fix the ``ZernikeMaskedFit()`` when passing masked data
 
 .. _lsst.ts.wep-1.5.1:
 

policy/cwfs/donutTemplateData/star.cmd

@@ -0,0 +1,12 @@
+backgroundmode 0
+raydensity 0.0
+perturbationmode 1
+trackingmode 0
+cleartracking
+clearclouds
+lascatprob 0.0
+contaminationmode 0
+diffractionmode 1
+straylight 0
+detectormode 0
+centroidfile 1