Organized util functions in utils directory.

doc/developer-guide/developer-guide.rst

@@ -51,8 +51,6 @@ This module is a high-level module to use other modules.
     :caption: Class diagram of wep
 
 * **WfEstimator**: Calculate the wavefront error in annular Zernike polynomials up to 22 terms based on the defocal donut images.
-* **Utility**: Utility functions used in WEP.
-* **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.
 * **DonutDetector**: Detect donuts directly from an out of focus image by convolution with a template image.
@@ -71,7 +69,6 @@ This module calculates the wavefront error by solving the TIE.
 * **CompensableImage**: Compensable image class to project the donut image from the image plane to the pupil plane.
 * **Image**: Image class to have the function to get the donut center.
 * **Instrument**: Instrument class to have the instrument information used in the Algorithm class to solve the TIE.
-* **Tool**: Annular Zernike polynomials related functions.
 * **CentroidFindFactory**: Factory for creating the centroid find object to calculate the centroid of donut.
 * **CentroidDefault**: Default centroid class.
 * **CentroidRandomWalk**: CentroidDefault child class to get the centroid of donut by the random walk model.
@@ -144,6 +141,20 @@ This module has the tasks to run WEP as a pipeline with Gen 3 LSST DM middleware
 * **GenerateDonutFromRefitWcsTaskConfig**: Configuration setup for GenerateDonutFromRefitWcsTask.
 * **GenerateDonutCatalogUtils**: Common utility functions for the GenerateDonutCatalog...Tasks.
 
+.. _WEP_modules_wep_utils:
+
+wep.utils
+-------------
+
+This module contains utility functions that are used elsewhere in WEP.
+
+* **enumUtils**: Enum definitions and related functions.
+* **ioUtils**: Functions for reading and writing files.
+* **taskUtils**: Functions for running command line tasks from a python script.
+* **zernikeUtils**: Functions for evaluating and fitting Zernike polynomials. 
+* **plotUtils**: Functions for plotting results.
+* **miscUtils**: Miscellaneous utility functions.
+
 .. _WEP_API:
 
 Python API reference
@@ -163,6 +174,9 @@ This section is autogenerated from docstrings.
 .. automodapi:: lsst.ts.wep.task
     :no-inheritance-diagram:
 
+.. automodapi:: lsst.ts.wep.utils
+    :no-inheritance-diagram:
+
 .. _WEP_contributing:
 
 Contributing

doc/versionHistory.rst

@@ -5,6 +5,15 @@
 ##################
 Version History
 ##################
+
+.. _lsst.ts.wep-7.0.0:
+
+-------------
+7.0.0
+-------------
+
+* Organize all utility functions inside the ``utils`` module.
+
 .. _lsst.ts.wep-6.4.12:
 
 -------------

python/lsst/ts/wep/__init__.py

@@ -1,5 +1,4 @@
 # -*- coding: utf-8 -*-
-from .utility import *
 
 # This class needs the scons to build the cython code. In the Jenkins test,
 # this will be a problem to import.

python/lsst/ts/wep/cwfs/__init__.py

@@ -13,4 +13,3 @@
 from .donutTemplatePhosim import *
 from .image import *
 from .instrument import *
-from .tool import *

python/lsst/ts/wep/cwfs/algorithm.py

@@ -27,15 +27,15 @@
 import galsim
 import numpy as np
 from lsst.ts.wep.cwfs.instrument import Instrument
-from lsst.ts.wep.cwfs.tool import (
+from lsst.ts.wep.paramReader import ParamReader
+from lsst.ts.wep.utils import (
+    DefocalType,
     ZernikeAnnularEval,
     ZernikeMaskedFit,
     extractArray,
     padArray,
+    plotZernike,
 )
-from lsst.ts.wep.paramReader import ParamReader
-from lsst.ts.wep.plotUtil import plotZernike
-from lsst.ts.wep.utility import DefocalType
 from scipy.ndimage import (
     binary_dilation,
     binary_erosion,

python/lsst/ts/wep/cwfs/baseCwfsTestCase.py

@@ -27,7 +27,7 @@
 from lsst.ts.wep.cwfs.algorithm import Algorithm
 from lsst.ts.wep.cwfs.compensableImage import CompensableImage
 from lsst.ts.wep.cwfs.instrument import Instrument
-from lsst.ts.wep.utility import DefocalType, getConfigDir
+from lsst.ts.wep.utils import DefocalType, getConfigDir
 
 
 class BaseCwfsTestCase(object):

python/lsst/ts/wep/cwfs/centroidFindFactory.py

@@ -24,7 +24,7 @@
 from lsst.ts.wep.cwfs.centroidConvolveTemplate import CentroidConvolveTemplate
 from lsst.ts.wep.cwfs.centroidOtsu import CentroidOtsu
 from lsst.ts.wep.cwfs.centroidRandomWalk import CentroidRandomWalk
-from lsst.ts.wep.utility import CentroidFindType
+from lsst.ts.wep.utils import CentroidFindType
 
 
 class CentroidFindFactory(object):

python/lsst/ts/wep/cwfs/compensableImage.py

@@ -28,14 +28,17 @@
 import numpy as np
 from galsim.utilities import horner2d
 from lsst.ts.wep.cwfs.image import Image
-from lsst.ts.wep.cwfs.tool import (
+from lsst.ts.wep.paramReader import ParamReader
+from lsst.ts.wep.utils import (
+    CentroidFindType,
+    DefocalType,
+    FilterType,
     ZernikeAnnularGrad,
     ZernikeAnnularJacobian,
     extractArray,
     padArray,
+    rotMatrix,
 )
-from lsst.ts.wep.paramReader import ParamReader
-from lsst.ts.wep.utility import CentroidFindType, DefocalType, FilterType, rotMatrix
 from scipy.interpolate import RectBivariateSpline
 from scipy.ndimage import (
     binary_dilation,

python/lsst/ts/wep/cwfs/donutTemplateFactory.py

@@ -23,7 +23,7 @@
 
 from lsst.ts.wep.cwfs.donutTemplateModel import DonutTemplateModel
 from lsst.ts.wep.cwfs.donutTemplatePhosim import DonutTemplatePhosim
-from lsst.ts.wep.utility import DonutTemplateType
+from lsst.ts.wep.utils import DonutTemplateType
 
 
 class DonutTemplateFactory(object):

python/lsst/ts/wep/cwfs/donutTemplateModel.py

@@ -27,7 +27,7 @@
 from lsst.ts.wep.cwfs.compensableImage import CompensableImage
 from lsst.ts.wep.cwfs.donutTemplateDefault import DonutTemplateDefault
 from lsst.ts.wep.cwfs.instrument import Instrument
-from lsst.ts.wep.utility import CamType, FilterType, getConfigDir, readPhoSimSettingData
+from lsst.ts.wep.utils import CamType, FilterType, getConfigDir, readPhoSimSettingData
 
 
 class DonutTemplateModel(DonutTemplateDefault):

python/lsst/ts/wep/cwfs/donutTemplatePhosim.py

@@ -25,7 +25,7 @@
 
 import numpy as np
 from lsst.ts.wep.cwfs.donutTemplateDefault import DonutTemplateDefault
-from lsst.ts.wep.utility import DefocalType, getConfigDir
+from lsst.ts.wep.utils import DefocalType, getConfigDir
 
 
 class DonutTemplatePhosim(DonutTemplateDefault):

python/lsst/ts/wep/cwfs/image.py

@@ -27,7 +27,7 @@
 import numpy as np
 from astropy.io import fits
 from lsst.ts.wep.cwfs.centroidFindFactory import CentroidFindFactory
-from lsst.ts.wep.utility import CentroidFindType
+from lsst.ts.wep.utils import CentroidFindType
 
 
 class Image(object):

python/lsst/ts/wep/cwfs/instrument.py

@@ -25,7 +25,7 @@
 
 import numpy as np
 from lsst.ts.wep.paramReader import ParamReader
-from lsst.ts.wep.utility import CamType, getCamNameFromCamType, getConfigDir
+from lsst.ts.wep.utils import CamType, getCamNameFromCamType, getConfigDir
 
 
 class Instrument(object):

python/lsst/ts/wep/deblend/deblendAdapt.py

@@ -25,7 +25,7 @@
 from lsst.ts.wep.cwfs.centroidFindFactory import CentroidFindFactory
 from lsst.ts.wep.deblend.deblendDefault import DeblendDefault
 from lsst.ts.wep.deblend.nelderMeadModify import nelderMeadModify
-from lsst.ts.wep.utility import CentroidFindType
+from lsst.ts.wep.utils import CentroidFindType
 from scipy.ndimage import (
     binary_closing,
     binary_erosion,

python/lsst/ts/wep/deblend/deblendDefault.py

@@ -23,7 +23,7 @@
 
 import numpy as np
 from lsst.ts.wep.cwfs.centroidFindFactory import CentroidFindFactory
-from lsst.ts.wep.utility import CentroidFindType
+from lsst.ts.wep.utils import CentroidFindType
 
 
 class DeblendDefault(object):

python/lsst/ts/wep/deblend/deblendDonutFactory.py

@@ -22,7 +22,7 @@
 __all__ = ["DeblendDonutFactory"]
 
 from lsst.ts.wep.deblend.deblendAdapt import DeblendAdapt
-from lsst.ts.wep.utility import DeblendDonutType
+from lsst.ts.wep.utils import DeblendDonutType
 
 
 class DeblendDonutFactory(object):

python/lsst/ts/wep/donutDetector.py

@@ -27,7 +27,7 @@
 import pandas as pd
 from lsst.ts.wep.cwfs.centroidFindFactory import CentroidFindFactory
 from lsst.ts.wep.deblend.deblendAdapt import DeblendAdapt
-from lsst.ts.wep.utility import CentroidFindType
+from lsst.ts.wep.utils import CentroidFindType
 from scipy.spatial.distance import cdist
 
 

python/lsst/ts/wep/task/calcZernikesTask.py

@@ -29,7 +29,7 @@
 from lsst.pipe.base import connectionTypes
 from lsst.ts.wep.task.combineZernikesSigmaClipTask import CombineZernikesSigmaClipTask
 from lsst.ts.wep.task.donutStamps import DonutStamps
-from lsst.ts.wep.utility import (
+from lsst.ts.wep.utils import (
     DefocalType,
     createInstDictFromConfig,
     getCamTypeFromButlerName,

python/lsst/ts/wep/task/cutOutDonutsBase.py

@@ -36,7 +36,7 @@
 from lsst.ts.wep.cwfs.instrument import Instrument
 from lsst.ts.wep.task.donutStamp import DonutStamp
 from lsst.ts.wep.task.donutStamps import DonutStamps
-from lsst.ts.wep.utility import (
+from lsst.ts.wep.utils import (
     DonutTemplateType,
     createInstDictFromConfig,
     getCamTypeFromButlerName,

python/lsst/ts/wep/task/cutOutDonutsCwfsTask.py

@@ -35,7 +35,7 @@
     CutOutDonutsBaseTaskConnections,
 )
 from lsst.ts.wep.task.donutStamps import DonutStamps
-from lsst.ts.wep.utility import DefocalType
+from lsst.ts.wep.utils import DefocalType
 from lsst.utils.timer import timeMethod
 
 

python/lsst/ts/wep/task/cutOutDonutsScienceSensorTask.py

@@ -39,7 +39,7 @@
     CutOutDonutsBaseTaskConnections,
 )
 from lsst.ts.wep.task.donutStamps import DonutStamps
-from lsst.ts.wep.utility import DefocalType
+from lsst.ts.wep.utils import DefocalType
 from lsst.utils.timer import timeMethod
 
 

python/lsst/ts/wep/task/donutSourceSelectorTask.py

@@ -32,7 +32,7 @@
 from lsst.afw.cameraGeom import FIELD_ANGLE, PIXELS
 from lsst.meas.algorithms.sourceSelector import _getFieldFromCatalog
 from lsst.ts.wep.paramReader import ParamReader
-from lsst.ts.wep.utility import getConfigDir
+from lsst.ts.wep.utils import getConfigDir
 from lsst.utils.timer import timeMethod
 from sklearn.neighbors import NearestNeighbors
 

python/lsst/ts/wep/task/donutStamp.py

@@ -32,7 +32,7 @@
 from lsst.afw.cameraGeom import FIELD_ANGLE, PIXELS
 from lsst.meas.algorithms.stamps import AbstractStamp
 from lsst.ts.wep.cwfs.compensableImage import CompensableImage
-from lsst.ts.wep.utility import DefocalType, FilterType, getFilterTypeFromBandLabel
+from lsst.ts.wep.utils import DefocalType, FilterType, getFilterTypeFromBandLabel
 
 
 @dataclass

python/lsst/ts/wep/task/generateDonutDirectDetectTask.py

@@ -34,7 +34,7 @@
 from lsst.ts.wep.cwfs.donutTemplateFactory import DonutTemplateFactory
 from lsst.ts.wep.task.donutQuickMeasurementTask import DonutQuickMeasurementTask
 from lsst.ts.wep.task.donutSourceSelectorTask import DonutSourceSelectorTask
-from lsst.ts.wep.utility import (
+from lsst.ts.wep.utils import (
     DefocalType,
     DonutTemplateType,
     createInstDictFromConfig,