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spacetelescope/drizzlepac | drizzlepac/wcs_functions.py | WCSMap.backward | def backward(self,pixx,pixy):
""" Transform pixx,pixy positions from the output frame back onto their
original positions in the input frame.
"""
skyx,skyy = self.output.wcs_pix2world(pixx,pixy,self.origin)
result = self.input.all_world2pix(skyx,skyy,self.origin)
retur... | python | def backward(self,pixx,pixy):
""" Transform pixx,pixy positions from the output frame back onto their
original positions in the input frame.
"""
skyx,skyy = self.output.wcs_pix2world(pixx,pixy,self.origin)
result = self.input.all_world2pix(skyx,skyy,self.origin)
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spacetelescope/drizzlepac | drizzlepac/staticMask.py | createMask | def createMask(input=None, static_sig=4.0, group=None, editpars=False, configObj=None, **inputDict):
""" The user can input a list of images if they like to create static masks
as well as optional values for static_sig and inputDict.
The configObj.cfg file will set the defaults and then override th... | python | def createMask(input=None, static_sig=4.0, group=None, editpars=False, configObj=None, **inputDict):
""" The user can input a list of images if they like to create static masks
as well as optional values for static_sig and inputDict.
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spacetelescope/drizzlepac | drizzlepac/staticMask.py | constructFilename | def constructFilename(signature):
"""Construct an output filename for the given signature::
signature=[instr+detector,(nx,ny),detnum]
The signature is in the image object.
"""
suffix = buildSignatureKey(signature)
filename = os.path.join('.', suffix)
return filename | python | def constructFilename(signature):
"""Construct an output filename for the given signature::
signature=[instr+detector,(nx,ny),detnum]
The signature is in the image object.
"""
suffix = buildSignatureKey(signature)
filename = os.path.join('.', suffix)
return filename | [
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spacetelescope/drizzlepac | drizzlepac/staticMask.py | staticMask.addMember | def addMember(self, imagePtr=None):
"""
Combines the input image with the static mask that
has the same signature.
Parameters
----------
imagePtr : object
An imageObject reference
Notes
-----
The signature parameter consists of the tu... | python | def addMember(self, imagePtr=None):
"""
Combines the input image with the static mask that
has the same signature.
Parameters
----------
imagePtr : object
An imageObject reference
Notes
-----
The signature parameter consists of the tu... | [
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spacetelescope/drizzlepac | drizzlepac/staticMask.py | staticMask.getMaskArray | def getMaskArray(self, signature):
""" Returns the appropriate StaticMask array for the image. """
if signature in self.masklist:
mask = self.masklist[signature]
else:
mask = None
return mask | python | def getMaskArray(self, signature):
""" Returns the appropriate StaticMask array for the image. """
if signature in self.masklist:
mask = self.masklist[signature]
else:
mask = None
return mask | [
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spacetelescope/drizzlepac | drizzlepac/staticMask.py | staticMask.getFilename | def getFilename(self,signature):
"""Returns the name of the output mask file that
should reside on disk for the given signature. """
filename=constructFilename(signature)
if(fileutil.checkFileExists(filename)):
return filename
else:
print("\nmMask file f... | python | def getFilename(self,signature):
"""Returns the name of the output mask file that
should reside on disk for the given signature. """
filename=constructFilename(signature)
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else:
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spacetelescope/drizzlepac | drizzlepac/staticMask.py | staticMask.close | def close(self):
""" Deletes all static mask objects. """
for key in self.masklist.keys():
self.masklist[key] = None
self.masklist = {} | python | def close(self):
""" Deletes all static mask objects. """
for key in self.masklist.keys():
self.masklist[key] = None
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spacetelescope/drizzlepac | drizzlepac/staticMask.py | staticMask.deleteMask | def deleteMask(self,signature):
""" Delete just the mask that matches the signature given."""
if signature in self.masklist:
self.masklist[signature] = None
else:
log.warning("No matching mask") | python | def deleteMask(self,signature):
""" Delete just the mask that matches the signature given."""
if signature in self.masklist:
self.masklist[signature] = None
else:
log.warning("No matching mask") | [
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spacetelescope/drizzlepac | drizzlepac/staticMask.py | staticMask.saveToFile | def saveToFile(self,imageObjectList):
""" Saves the static mask to a file
it uses the signatures associated with each
mask to contruct the filename for the output mask image.
"""
virtual = imageObjectList[0].inmemory
for key in self.masklist.keys():
#... | python | def saveToFile(self,imageObjectList):
""" Saves the static mask to a file
it uses the signatures associated with each
mask to contruct the filename for the output mask image.
"""
virtual = imageObjectList[0].inmemory
for key in self.masklist.keys():
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spacetelescope/drizzlepac | drizzlepac/stisData.py | expand_image | def expand_image(image, shape):
""" Expand image from original shape to requested shape. Output shape
must be an integer multiple of input image shape for each axis. """
if (shape[0] % image.shape[0]) or (shape[1] % image.shape[1]):
raise ValueError("Output shape must be an integer multiple of input... | python | def expand_image(image, shape):
""" Expand image from original shape to requested shape. Output shape
must be an integer multiple of input image shape for each axis. """
if (shape[0] % image.shape[0]) or (shape[1] % image.shape[1]):
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spacetelescope/drizzlepac | drizzlepac/stisData.py | bilinear_interp | def bilinear_interp(data, x, y):
""" Interpolate input ``data`` at "pixel" coordinates ``x`` and ``y``. """
x = np.asarray(x)
y = np.asarray(y)
if x.shape != y.shape:
raise ValueError("X- and Y-coordinates must have identical shapes.")
out_shape = x.shape
out_size = x.size
x = x.rav... | python | def bilinear_interp(data, x, y):
""" Interpolate input ``data`` at "pixel" coordinates ``x`` and ``y``. """
x = np.asarray(x)
y = np.asarray(y)
if x.shape != y.shape:
raise ValueError("X- and Y-coordinates must have identical shapes.")
out_shape = x.shape
out_size = x.size
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spacetelescope/drizzlepac | drizzlepac/stisData.py | STISInputImage.getflat | def getflat(self, chip):
"""
Method for retrieving a detector's flat field. For STIS there are three.
This method will return an array the same shape as the image.
"""
sci_chip = self._image[self.scienceExt,chip]
exten = self.errExt+','+str(chip)
# The keyword f... | python | def getflat(self, chip):
"""
Method for retrieving a detector's flat field. For STIS there are three.
This method will return an array the same shape as the image.
"""
sci_chip = self._image[self.scienceExt,chip]
exten = self.errExt+','+str(chip)
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spacetelescope/drizzlepac | drizzlepac/stisData.py | STISInputImage._assignSignature | def _assignSignature(self, chip):
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spacetelescope/drizzlepac | drizzlepac/stisData.py | CCDInputImage.getReadNoise | def getReadNoise(self):
"""
Method for returning the readnoise of a detector (in DN).
:units: DN
This should work on a chip, since different chips to be consistant with other
detector classes where different chips have different gains.
"""
if self.proc_unit == ... | python | def getReadNoise(self):
"""
Method for returning the readnoise of a detector (in DN).
:units: DN
This should work on a chip, since different chips to be consistant with other
detector classes where different chips have different gains.
"""
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spacetelescope/drizzlepac | drizzlepac/stisData.py | CCDInputImage.setInstrumentParameters | def setInstrumentParameters(self, instrpars):
""" This method overrides the superclass to set default values into
the parameter dictionary, in case empty entries are provided.
"""
pri_header = self._image[0].header
if self._isNotValid (instrpars['gain'], instrpars['gnkeyword... | python | def setInstrumentParameters(self, instrpars):
""" This method overrides the superclass to set default values into
the parameter dictionary, in case empty entries are provided.
"""
pri_header = self._image[0].header
if self._isNotValid (instrpars['gain'], instrpars['gnkeyword... | [
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spacetelescope/drizzlepac | drizzlepac/stisData.py | NUVInputImage.doUnitConversions | def doUnitConversions(self):
"""Convert the data to electrons.
This converts all science data extensions and saves
the results back to disk. We need to make sure
the data inside the chips already in memory is altered as well.
"""
for det in range(1,self._numchips+1,1):
... | python | def doUnitConversions(self):
"""Convert the data to electrons.
This converts all science data extensions and saves
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spacetelescope/drizzlepac | drizzlepac/hlautils/analyze.py | analyze_data | def analyze_data(inputFileList, **kwargs):
"""
Determine if images within the dataset can be aligned
Parameters
==========
inputFileList: list
List containing FLT and/or FLC filenames for all input images which comprise an associated
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"""
Determine if images within the dataset can be aligned
Parameters
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inputFileList: list
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spacetelescope/drizzlepac | drizzlepac/hlautils/analyze.py | generate_msg | def generate_msg(filename, msg, key, value):
""" Generate a message for the output log indicating the file/association will not
be processed as the characteristics of the data are known to be inconsistent
with alignment.
"""
log.info('Dataset ' + filename + ' has (keyword = value) of (' + k... | python | def generate_msg(filename, msg, key, value):
""" Generate a message for the output log indicating the file/association will not
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spacetelescope/drizzlepac | drizzlepac/drizCR.py | drizCR | def drizCR(input=None, configObj=None, editpars=False, **inputDict):
""" Look for cosmic rays. """
log.debug(inputDict)
inputDict["input"] = input
configObj = util.getDefaultConfigObj(__taskname__, configObj, inputDict,
loadOnly=(not editpars))
if configObj i... | python | def drizCR(input=None, configObj=None, editpars=False, **inputDict):
""" Look for cosmic rays. """
log.debug(inputDict)
inputDict["input"] = input
configObj = util.getDefaultConfigObj(__taskname__, configObj, inputDict,
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spacetelescope/drizzlepac | drizzlepac/drizCR.py | _driz_cr | def _driz_cr(sciImage, virtual_outputs, paramDict):
"""mask blemishes in dithered data by comparison of an image
with a model image and the derivative of the model image.
- ``sciImage`` is an imageObject which contains the science data
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"""mask blemishes in dithered data by comparison of an image
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spacetelescope/drizzlepac | drizzlepac/drizCR.py | createCorrFile | def createCorrFile(outfile, arrlist, template):
"""
Create a _cor file with the same format as the original input image.
The DQ array will be replaced with the mask array used to create the _cor
file.
"""
# Remove the existing cor file if it exists
if os.path.isfile(outfile):
os.rem... | python | def createCorrFile(outfile, arrlist, template):
"""
Create a _cor file with the same format as the original input image.
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file.
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spacetelescope/drizzlepac | drizzlepac/drizCR.py | setDefaults | def setDefaults(configObj={}):
""" Return a dictionary of the default parameters
which also been updated with the user overrides.
"""
paramDict = {
'gain': 7, # Detector gain, e-/ADU
'grow': 1, # Radius around CR pixel to mask [default=1 for
... | python | def setDefaults(configObj={}):
""" Return a dictionary of the default parameters
which also been updated with the user overrides.
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paramDict = {
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spacetelescope/drizzlepac | drizzlepac/drizCR.py | help | def help(file=None):
"""
Print out syntax help for running ``astrodrizzle``
Parameters
----------
file : str (Default = None)
If given, write out help to the filename specified by this parameter
Any previously existing file with this name will be deleted before
writing out t... | python | def help(file=None):
"""
Print out syntax help for running ``astrodrizzle``
Parameters
----------
file : str (Default = None)
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spacetelescope/drizzlepac | drizzlepac/drizCR.py | getHelpAsString | def getHelpAsString(docstring=False, show_ver=True):
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"""
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spacetelescope/drizzlepac | drizzlepac/processInput.py | setCommonInput | def setCommonInput(configObj, createOutwcs=True):
"""
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spacetelescope/drizzlepac | drizzlepac/processInput.py | reportResourceUsage | def reportResourceUsage(imageObjectList, outwcs, num_cores,
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"""
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spacetelescope/drizzlepac | drizzlepac/processInput.py | getMdriztabPars | def getMdriztabPars(input):
""" High-level function for getting the parameters from MDRIZTAB
Used primarily for TEAL interface.
"""
filelist,output,ivmlist,oldasndict=processFilenames(input,None)
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""" High-level function for getting the parameters from MDRIZTAB
Used primarily for TEAL interface.
"""
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spacetelescope/drizzlepac | drizzlepac/processInput.py | addIVMInputs | def addIVMInputs(imageObjectList,ivmlist):
""" Add IVM filenames provided by user to outputNames dictionary for each input imageObject.
"""
if ivmlist is None:
return
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""" Add IVM filenames provided by user to outputNames dictionary for each input imageObject.
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spacetelescope/drizzlepac | drizzlepac/processInput.py | checkMultipleFiles | def checkMultipleFiles(input):
""" Evaluates the input to determine whether there is 1 or more than 1 valid input file.
"""
f,i,o,a=buildFileList(input)
return len(f) > 1 | python | def checkMultipleFiles(input):
""" Evaluates the input to determine whether there is 1 or more than 1 valid input file.
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spacetelescope/drizzlepac | drizzlepac/processInput.py | createImageObjectList | def createImageObjectList(files,instrpars,group=None,
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""" Returns a list of imageObject instances, 1 for each input image in the list of input filenames.
"""
imageObjList = []
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imageObjList = []
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spacetelescope/drizzlepac | drizzlepac/processInput.py | _getInputImage | def _getInputImage (input,group=None):
""" Factory function to return appropriate imageObject class instance"""
# extract primary header and SCI,1 header from input image
sci_ext = 'SCI'
if group in [None,'']:
exten = '[sci,1]'
phdu = fits.getheader(input, memmap=False)
else:
... | python | def _getInputImage (input,group=None):
""" Factory function to return appropriate imageObject class instance"""
# extract primary header and SCI,1 header from input image
sci_ext = 'SCI'
if group in [None,'']:
exten = '[sci,1]'
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spacetelescope/drizzlepac | drizzlepac/processInput.py | processFilenames | def processFilenames(input=None,output=None,infilesOnly=False):
"""Process the input string which contains the input file information and
return a filelist,output
"""
ivmlist = None
oldasndict = None
if input is None:
print("No input files provided to processInput")
raise Val... | python | def processFilenames(input=None,output=None,infilesOnly=False):
"""Process the input string which contains the input file information and
return a filelist,output
"""
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spacetelescope/drizzlepac | drizzlepac/processInput.py | process_input | def process_input(input, output=None, ivmlist=None, updatewcs=True,
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"""
Create the full input list of filenames after verifying and converting
files as needed.
"""
newfilelist, ivmlist, output, oldasndict, origflist = buildFileListOrig... | python | def process_input(input, output=None, ivmlist=None, updatewcs=True,
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Create the full input list of filenames after verifying and converting
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spacetelescope/drizzlepac | drizzlepac/processInput.py | _process_input_wcs | def _process_input_wcs(infiles, wcskey, updatewcs):
"""
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portion of input handling which sets/updates WCS data, and is a performance
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"""
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"""
This is a subset of process_input(), for internal use only. This is the
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spacetelescope/drizzlepac | drizzlepac/processInput.py | _process_input_wcs_single | def _process_input_wcs_single(fname, wcskey, updatewcs):
"""
See docs for _process_input_wcs.
This is separated to be spawned in parallel.
"""
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"""
See docs for _process_input_wcs.
This is separated to be spawned in parallel.
"""
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spacetelescope/drizzlepac | drizzlepac/processInput.py | buildFileList | def buildFileList(input, output=None, ivmlist=None,
wcskey=None, updatewcs=True, **workinplace):
"""
Builds a file list which has undergone various instrument-specific
checks for input to MultiDrizzle, including splitting STIS associations.
"""
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Builds a file list which has undergone various instrument-specific
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spacetelescope/drizzlepac | drizzlepac/processInput.py | buildFileListOrig | def buildFileListOrig(input, output=None, ivmlist=None,
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"""
Builds a file list which has undergone various instrument-specific
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spacetelescope/drizzlepac | drizzlepac/processInput.py | buildASNList | def buildASNList(rootnames, asnname, check_for_duplicates=True):
"""
Return the list of filenames for a given set of rootnames
"""
# Recognize when multiple valid inputs with the same rootname are present
# this would happen when both CTE-corrected (_flc) and non-CTE-corrected (_flt)
# products... | python | def buildASNList(rootnames, asnname, check_for_duplicates=True):
"""
Return the list of filenames for a given set of rootnames
"""
# Recognize when multiple valid inputs with the same rootname are present
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spacetelescope/drizzlepac | drizzlepac/processInput.py | changeSuffixinASN | def changeSuffixinASN(asnfile, suffix):
"""
Create a copy of the original asn file and change the name of all members
to include the suffix.
"""
# Start by creating a new name for the ASN table
_new_asn = asnfile.replace('_asn.fits','_'+suffix+'_asn.fits')
if os.path.exists(_new_asn):
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"""
Create a copy of the original asn file and change the name of all members
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"""
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_new_asn = asnfile.replace('_asn.fits','_'+suffix+'_asn.fits')
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spacetelescope/drizzlepac | drizzlepac/processInput.py | checkForDuplicateInputs | def checkForDuplicateInputs(rootnames):
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"""
flist = []
duplist = []
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# Look for any recognized CTE-corrected products
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Check input files specified in ASN table for duplicate versions with
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spacetelescope/drizzlepac | drizzlepac/processInput.py | resetDQBits | def resetDQBits(imageObjectList, cr_bits_value=4096):
"""Reset the CR bit in each input image's DQ array"""
if cr_bits_value > 0:
for img in imageObjectList:
for chip in range(1,img._numchips+1,1):
sci_chip = img._image[img.scienceExt,chip]
resetbits.reset_dq... | python | def resetDQBits(imageObjectList, cr_bits_value=4096):
"""Reset the CR bit in each input image's DQ array"""
if cr_bits_value > 0:
for img in imageObjectList:
for chip in range(1,img._numchips+1,1):
sci_chip = img._image[img.scienceExt,chip]
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spacetelescope/drizzlepac | drizzlepac/processInput.py | update_member_names | def update_member_names(oldasndict, pydr_input):
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spacetelescope/drizzlepac | drizzlepac/processInput.py | manageInputCopies | def manageInputCopies(filelist, **workinplace):
"""
Creates copies of all input images in a sub-directory.
The copies are made prior to any processing being done to the images at all,
including updating the WCS keywords. If there are already copies present,
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"""
Creates copies of all input images in a sub-directory.
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spacetelescope/drizzlepac | drizzlepac/processInput.py | buildEmptyDRZ | def buildEmptyDRZ(input, output):
"""
Create an empty DRZ file.
This module creates an empty DRZ file in a valid FITS format so that the HST
pipeline can handle the Multidrizzle zero expossure time exception
where all data has been excluded from processing.
Parameters
----------
input ... | python | def buildEmptyDRZ(input, output):
"""
Create an empty DRZ file.
This module creates an empty DRZ file in a valid FITS format so that the HST
pipeline can handle the Multidrizzle zero expossure time exception
where all data has been excluded from processing.
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spacetelescope/drizzlepac | drizzlepac/processInput.py | checkDGEOFile | def checkDGEOFile(filenames):
"""
Verify that input file has been updated with NPOLFILE
This function checks for the presence of 'NPOLFILE' kw in the primary header
when 'DGEOFILE' kw is present and valid (i.e. 'DGEOFILE' is not blank or 'N/A').
It handles the case of science files downloaded from ... | python | def checkDGEOFile(filenames):
"""
Verify that input file has been updated with NPOLFILE
This function checks for the presence of 'NPOLFILE' kw in the primary header
when 'DGEOFILE' kw is present and valid (i.e. 'DGEOFILE' is not blank or 'N/A').
It handles the case of science files downloaded from ... | [
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spacetelescope/drizzlepac | drizzlepac/processInput.py | _setDefaults | def _setDefaults(input_dict={}):
""" Define full set of default values for unit-testing this module.[OBSOLETE]"""
paramDict = {
'input':'*flt.fits',
'output':None,
'mdriztab':None,
'refimage':None,
'runfile':None,
'workinplace':False,
'updatewcs':True,
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""" Define full set of default values for unit-testing this module.[OBSOLETE]"""
paramDict = {
'input':'*flt.fits',
'output':None,
'mdriztab':None,
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'runfile':None,
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spacetelescope/drizzlepac | drizzlepac/nicmosData.py | NICMOSInputImage.getdarkimg | def getdarkimg(self,chip):
"""
Return an array representing the dark image for the detector.
Returns
-------
dark : array
The dark array in the same shape as the image with **units of cps**.
"""
# Read the temperature dependeant dark file. The name... | python | def getdarkimg(self,chip):
"""
Return an array representing the dark image for the detector.
Returns
-------
dark : array
The dark array in the same shape as the image with **units of cps**.
"""
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spacetelescope/drizzlepac | drizzlepac/nicmosData.py | NICMOSInputImage.isCountRate | def isCountRate(self):
"""
isCountRate: Method or IRInputObject used to indicate if the
science data is in units of counts or count rate. This method
assumes that the keyword 'BUNIT' is in the header of the input
FITS file.
"""
has_bunit = False
if 'BUNIT... | python | def isCountRate(self):
"""
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science data is in units of counts or count rate. This method
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FITS file.
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spacetelescope/drizzlepac | drizzlepac/nicmosData.py | NIC2InputImage.setInstrumentParameters | def setInstrumentParameters(self, instrpars):
""" This method overrides the superclass to set default values into
the parameter dictionary, in case empty entries are provided.
"""
pri_header = self._image[0].header
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spacetelescope/drizzlepac | drizzlepac/photeq.py | photeq | def photeq(files='*_flt.fits', sciext='SCI', errext='ERR',
ref_phot=None, ref_phot_ext=None,
phot_kwd='PHOTFLAM', aux_phot_kwd='PHOTFNU',
search_primary=True,
readonly=True, clobber=False, logfile='photeq.log'):
"""
Adjust data values of images by equalizing each chip... | python | def photeq(files='*_flt.fits', sciext='SCI', errext='ERR',
ref_phot=None, ref_phot_ext=None,
phot_kwd='PHOTFLAM', aux_phot_kwd='PHOTFNU',
search_primary=True,
readonly=True, clobber=False, logfile='photeq.log'):
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spacetelescope/drizzlepac | drizzlepac/tweakreg.py | _managePsets | def _managePsets(configobj, section_name, task_name, iparsobj=None, input_dict=None):
""" Read in parameter values from PSET-like configobj tasks defined for
source-finding algorithms, and any other PSET-like tasks under this task,
and merge those values into the input configobj dictionary.
"""
... | python | def _managePsets(configobj, section_name, task_name, iparsobj=None, input_dict=None):
""" Read in parameter values from PSET-like configobj tasks defined for
source-finding algorithms, and any other PSET-like tasks under this task,
and merge those values into the input configobj dictionary.
"""
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spacetelescope/drizzlepac | drizzlepac/tweakreg.py | edit_imagefindpars | def edit_imagefindpars():
""" Allows the user to edit the imagefindpars configObj in a TEAL GUI
"""
teal.teal(imagefindpars.__taskname__, returnAs=None,
autoClose=True, loadOnly=False, canExecute=False) | python | def edit_imagefindpars():
""" Allows the user to edit the imagefindpars configObj in a TEAL GUI
"""
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spacetelescope/drizzlepac | drizzlepac/tweakreg.py | edit_refimagefindpars | def edit_refimagefindpars():
""" Allows the user to edit the refimagefindpars configObj in a TEAL GUI
"""
teal.teal(refimagefindpars.__taskname__, returnAs=None,
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""" Allows the user to edit the refimagefindpars configObj in a TEAL GUI
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spacetelescope/drizzlepac | drizzlepac/tweakreg.py | run | def run(configobj):
""" Primary Python interface for image registration code
This task replaces 'tweakshifts'
"""
print('TweakReg Version %s(%s) started at: %s \n'%(
__version__,__version_date__,util._ptime()[0]))
util.print_pkg_versions()
# make sure 'updatewcs' is set ... | python | def run(configobj):
""" Primary Python interface for image registration code
This task replaces 'tweakshifts'
"""
print('TweakReg Version %s(%s) started at: %s \n'%(
__version__,__version_date__,util._ptime()[0]))
util.print_pkg_versions()
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spacetelescope/drizzlepac | drizzlepac/hlautils/get_git_rev_info.py | print_rev_id | def print_rev_id(localRepoPath):
"""prints information about the specified local repository to STDOUT. Expected method of execution: command-line or
shell script call
Parameters
----------
localRepoPath: string
Local repository path.
Returns
=======
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"""prints information about the specified local repository to STDOUT. Expected method of execution: command-line or
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Parameters
----------
localRepoPath: string
Local repository path.
Returns
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spacetelescope/drizzlepac | drizzlepac/hlautils/get_git_rev_info.py | get_rev_id | def get_rev_id(localRepoPath):
"""returns the current full git revision id of the specified local repository. Expected method of execution: python
subroutine call
Parameters
----------
localRepoPath: string
Local repository path.
Returns
=======
full git revision ID of the spec... | python | def get_rev_id(localRepoPath):
"""returns the current full git revision id of the specified local repository. Expected method of execution: python
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localRepoPath: string
Local repository path.
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spacetelescope/drizzlepac | drizzlepac/updatenpol.py | update | def update(input,refdir="jref$",local=None,interactive=False,wcsupdate=True):
"""
Updates headers of files given as input to point to the new reference files
NPOLFILE and D2IMFILE required with the new C version of MultiDrizzle.
Parameters
-----------
input : string or list
Name... | python | def update(input,refdir="jref$",local=None,interactive=False,wcsupdate=True):
"""
Updates headers of files given as input to point to the new reference files
NPOLFILE and D2IMFILE required with the new C version of MultiDrizzle.
Parameters
-----------
input : string or list
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spacetelescope/drizzlepac | drizzlepac/updatenpol.py | find_d2ifile | def find_d2ifile(flist,detector):
""" Search a list of files for one that matches the detector specified.
"""
d2ifile = None
for f in flist:
fdet = fits.getval(f, 'detector', memmap=False)
if fdet == detector:
d2ifile = f
return d2ifile | python | def find_d2ifile(flist,detector):
""" Search a list of files for one that matches the detector specified.
"""
d2ifile = None
for f in flist:
fdet = fits.getval(f, 'detector', memmap=False)
if fdet == detector:
d2ifile = f
return d2ifile | [
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spacetelescope/drizzlepac | drizzlepac/updatenpol.py | find_npolfile | def find_npolfile(flist,detector,filters):
""" Search a list of files for one that matches the configuration
of detector and filters used.
"""
npolfile = None
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if fdet == detector:
filt1 = fits.getval(f, '... | python | def find_npolfile(flist,detector,filters):
""" Search a list of files for one that matches the configuration
of detector and filters used.
"""
npolfile = None
for f in flist:
fdet = fits.getval(f, 'detector', memmap=False)
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spacetelescope/drizzlepac | drizzlepac/updatenpol.py | run | def run(configobj=None,editpars=False):
""" Teal interface for running this code.
"""
if configobj is None:
configobj =teal.teal(__taskname__,loadOnly=(not editpars))
update(configobj['input'],configobj['refdir'],
local=configobj['local'],interactive=configobj['interactive'],
w... | python | def run(configobj=None,editpars=False):
""" Teal interface for running this code.
"""
if configobj is None:
configobj =teal.teal(__taskname__,loadOnly=(not editpars))
update(configobj['input'],configobj['refdir'],
local=configobj['local'],interactive=configobj['interactive'],
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spacetelescope/drizzlepac | drizzlepac/hlautils/astroquery_utils.py | retrieve_observation | def retrieve_observation(obsid, suffix=['FLC'], archive=False,clobber=False):
"""Simple interface for retrieving an observation from the MAST archive
If the input obsid is for an association, it will request all members with
the specified suffixes.
Parameters
-----------
obsid : string
... | python | def retrieve_observation(obsid, suffix=['FLC'], archive=False,clobber=False):
"""Simple interface for retrieving an observation from the MAST archive
If the input obsid is for an association, it will request all members with
the specified suffixes.
Parameters
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obsid : string
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spacetelescope/drizzlepac | drizzlepac/resetbits.py | reset_dq_bits | def reset_dq_bits(input,bits,extver=None,extname='dq'):
""" This function resets bits in the integer array(s) of a FITS file.
Parameters
----------
filename : str
full filename with path
bits : str
sum or list of integers corresponding to all the bits to be reset
extver : int,... | python | def reset_dq_bits(input,bits,extver=None,extname='dq'):
""" This function resets bits in the integer array(s) of a FITS file.
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----------
filename : str
full filename with path
bits : str
sum or list of integers corresponding to all the bits to be reset
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spacetelescope/drizzlepac | drizzlepac/pixreplace.py | replace | def replace(input, **pars):
""" Replace pixels in `input` that have a value of `pixvalue`
with a value given by `newvalue`.
"""
pixvalue = pars.get('pixvalue', np.nan)
if pixvalue is None: pixvalue = np.nan # insure that None == np.nan
newvalue = pars.get('newvalue', 0.0)
ext = pars.g... | python | def replace(input, **pars):
""" Replace pixels in `input` that have a value of `pixvalue`
with a value given by `newvalue`.
"""
pixvalue = pars.get('pixvalue', np.nan)
if pixvalue is None: pixvalue = np.nan # insure that None == np.nan
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spacetelescope/drizzlepac | drizzlepac/tweakback.py | tweakback | def tweakback(drzfile, input=None, origwcs = None,
newname = None, wcsname = None,
extname='SCI', force=False, verbose=False):
"""
Apply WCS solution recorded in drizzled file to distorted input images
(``_flt.fits`` files) used to create the drizzled file. This task relies... | python | def tweakback(drzfile, input=None, origwcs = None,
newname = None, wcsname = None,
extname='SCI', force=False, verbose=False):
"""
Apply WCS solution recorded in drizzled file to distorted input images
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spacetelescope/drizzlepac | drizzlepac/tweakback.py | extract_input_filenames | def extract_input_filenames(drzfile):
"""
Generate a list of filenames from a drizzled image's header
"""
data_kws = fits.getval(drzfile, 'd*data', ext=0, memmap=False)
if len(data_kws) == 0:
return None
fnames = []
for kw in data_kws.cards:
f = kw.value.split('[')[0]
... | python | def extract_input_filenames(drzfile):
"""
Generate a list of filenames from a drizzled image's header
"""
data_kws = fits.getval(drzfile, 'd*data', ext=0, memmap=False)
if len(data_kws) == 0:
return None
fnames = []
for kw in data_kws.cards:
f = kw.value.split('[')[0]
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spacetelescope/drizzlepac | drizzlepac/tweakback.py | determine_orig_wcsname | def determine_orig_wcsname(header, wnames, wkeys):
"""
Determine the name of the original, unmodified WCS solution
"""
orig_wcsname = None
orig_key = None
if orig_wcsname is None:
for k,w in wnames.items():
if w[:4] == 'IDC_':
orig_wcsname = w
... | python | def determine_orig_wcsname(header, wnames, wkeys):
"""
Determine the name of the original, unmodified WCS solution
"""
orig_wcsname = None
orig_key = None
if orig_wcsname is None:
for k,w in wnames.items():
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | parse_atfile_cat | def parse_atfile_cat(input):
"""
Return the list of catalog filenames specified as part of the input @-file
"""
with open(input[1:]) as f:
catlist = []
catdict = {}
for line in f.readlines():
if line[0] == '#' or not line.strip():
continue
... | python | def parse_atfile_cat(input):
"""
Return the list of catalog filenames specified as part of the input @-file
"""
with open(input[1:]) as f:
catlist = []
catdict = {}
for line in f.readlines():
if line[0] == '#' or not line.strip():
continue
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | parse_skypos | def parse_skypos(ra, dec):
"""
Function to parse RA and Dec input values and turn them into decimal
degrees
Input formats could be:
["nn","nn","nn.nn"]
"nn nn nn.nnn"
"nn:nn:nn.nn"
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nn.nnnnnnnn
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"""
... | python | def parse_skypos(ra, dec):
"""
Function to parse RA and Dec input values and turn them into decimal
degrees
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["nn","nn","nn.nn"]
"nn nn nn.nnn"
"nn:nn:nn.nn"
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | radec_hmstodd | def radec_hmstodd(ra, dec):
""" Function to convert HMS values into decimal degrees.
This function relies on the astropy.coordinates package to perform the
conversion to decimal degrees.
Parameters
----------
ra : list or array
List or array of input RA positio... | python | def radec_hmstodd(ra, dec):
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | parse_exclusions | def parse_exclusions(exclusions):
""" Read in exclusion definitions from file named by 'exclusions'
and return a list of positions and distances
"""
fname = fileutil.osfn(exclusions)
if os.path.exists(fname):
with open(fname) as f:
flines = f.readlines()
else:
pri... | python | def parse_exclusions(exclusions):
""" Read in exclusion definitions from file named by 'exclusions'
and return a list of positions and distances
"""
fname = fileutil.osfn(exclusions)
if os.path.exists(fname):
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | parse_colname | def parse_colname(colname):
""" Common function to interpret input column names provided by the user.
This function translates column specification provided by the user
into a column number.
Notes
-----
This function will understand the following inputs::
'1,2,... | python | def parse_colname(colname):
""" Common function to interpret input column names provided by the user.
This function translates column specification provided by the user
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Notes
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | readcols | def readcols(infile, cols=None):
""" Function which reads specified columns from either FITS tables or
ASCII files
This function reads in the columns specified by the user into numpy
arrays regardless of the format of the input table (ASCII or FITS
table).
Parameters
... | python | def readcols(infile, cols=None):
""" Function which reads specified columns from either FITS tables or
ASCII files
This function reads in the columns specified by the user into numpy
arrays regardless of the format of the input table (ASCII or FITS
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | read_FITS_cols | def read_FITS_cols(infile, cols=None): # noqa: N802
""" Read columns from FITS table """
with fits.open(infile, memmap=False) as ftab:
extnum = 0
extfound = False
for extn in ftab:
if 'tfields' in extn.header:
extfound = True
break
... | python | def read_FITS_cols(infile, cols=None): # noqa: N802
""" Read columns from FITS table """
with fits.open(infile, memmap=False) as ftab:
extnum = 0
extfound = False
for extn in ftab:
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | read_ASCII_cols | def read_ASCII_cols(infile, cols=[1, 2, 3]): # noqa: N802
""" Interpret input ASCII file to return arrays for specified columns.
Notes
-----
The specification of the columns should be expected to have lists for
each 'column', with all columns in each list combined into a single
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""" Interpret input ASCII file to return arrays for specified columns.
Notes
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | write_shiftfile | def write_shiftfile(image_list, filename, outwcs='tweak_wcs.fits'):
""" Write out a shiftfile for a given list of input Image class objects
"""
rows = ''
nrows = 0
for img in image_list:
row = img.get_shiftfile_row()
if row is not None:
rows += row
nrows += 1
... | python | def write_shiftfile(image_list, filename, outwcs='tweak_wcs.fits'):
""" Write out a shiftfile for a given list of input Image class objects
"""
rows = ''
nrows = 0
for img in image_list:
row = img.get_shiftfile_row()
if row is not None:
rows += row
nrows += 1
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | createWcsHDU | def createWcsHDU(wcs): # noqa: N802
""" Generate a WCS header object that can be used to populate a reference
WCS HDU.
For most applications, stwcs.wcsutil.HSTWCS.wcs2header()
will work just as well.
"""
header = wcs.to_header()
header['EXTNAME'] = 'WCS'
header['EXTVER'] = 1
# No... | python | def createWcsHDU(wcs): # noqa: N802
""" Generate a WCS header object that can be used to populate a reference
WCS HDU.
For most applications, stwcs.wcsutil.HSTWCS.wcs2header()
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header = wcs.to_header()
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | gauss_array | def gauss_array(nx, ny=None, fwhm=1.0, sigma_x=None, sigma_y=None,
zero_norm=False):
""" Computes the 2D Gaussian with size nx*ny.
Parameters
----------
nx : int
ny : int [Default: None]
Size of output array for the generated Gaussian. If ny == None,
... | python | def gauss_array(nx, ny=None, fwhm=1.0, sigma_x=None, sigma_y=None,
zero_norm=False):
""" Computes the 2D Gaussian with size nx*ny.
Parameters
----------
nx : int
ny : int [Default: None]
Size of output array for the generated Gaussian. If ny == None,
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | gauss | def gauss(x, sigma):
""" Compute 1-D value of gaussian at position x relative to center."""
return (np.exp(-np.power(x, 2) / (2 * np.power(sigma, 2))) /
(sigma * np.sqrt(2 * np.pi))) | python | def gauss(x, sigma):
""" Compute 1-D value of gaussian at position x relative to center."""
return (np.exp(-np.power(x, 2) / (2 * np.power(sigma, 2))) /
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | make_vector_plot | def make_vector_plot(coordfile, columns=[1, 2, 3, 4], data=None,
figure_id=None, title=None, axes=None, every=1,
labelsize=8, ylimit=None, limit=None, xlower=None,
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figure_id=None, title=None, axes=None, every=1,
labelsize=8, ylimit=None, limit=None, xlower=None,
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | find_xy_peak | def find_xy_peak(img, center=None, sigma=3.0):
""" Find the center of the peak of offsets """
# find level of noise in histogram
istats = imagestats.ImageStats(img.astype(np.float32), nclip=1,
fields='stddev,mode,mean,max,min')
if istats.stddev == 0.0:
istats =... | python | def find_xy_peak(img, center=None, sigma=3.0):
""" Find the center of the peak of offsets """
# find level of noise in histogram
istats = imagestats.ImageStats(img.astype(np.float32), nclip=1,
fields='stddev,mode,mean,max,min')
if istats.stddev == 0.0:
istats =... | [
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | plot_zeropoint | def plot_zeropoint(pars):
""" Plot 2d histogram.
Pars will be a dictionary containing:
data, figure_id, vmax, title_str, xp,yp, searchrad
"""
from matplotlib import pyplot as plt
xp = pars['xp']
yp = pars['yp']
searchrad = int(pars['searchrad'] + 0.5)
plt.figure(num=pars['figu... | python | def plot_zeropoint(pars):
""" Plot 2d histogram.
Pars will be a dictionary containing:
data, figure_id, vmax, title_str, xp,yp, searchrad
"""
from matplotlib import pyplot as plt
xp = pars['xp']
yp = pars['yp']
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | build_xy_zeropoint | def build_xy_zeropoint(imgxy, refxy, searchrad=3.0, histplot=False,
figure_id=1, plotname=None, interactive=True):
""" Create a matrix which contains the delta between each XY position and
each UV position.
"""
print('Computing initial guess for X and Y shifts...')
# run ... | python | def build_xy_zeropoint(imgxy, refxy, searchrad=3.0, histplot=False,
figure_id=1, plotname=None, interactive=True):
""" Create a matrix which contains the delta between each XY position and
each UV position.
"""
print('Computing initial guess for X and Y shifts...')
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spacetelescope/drizzlepac | drizzlepac/tweakutils.py | build_pos_grid | def build_pos_grid(start, end, nstep, mesh=False):
"""
Return a grid of positions starting at X,Y given by 'start', and ending
at X,Y given by 'end'. The grid will be completely filled in X and Y by
every 'step' interval.
"""
# Build X and Y arrays
dx = end[0] - start[0]
if dx < 0:
... | python | def build_pos_grid(start, end, nstep, mesh=False):
"""
Return a grid of positions starting at X,Y given by 'start', and ending
at X,Y given by 'end'. The grid will be completely filled in X and Y by
every 'step' interval.
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spacetelescope/drizzlepac | drizzlepac/wfpc2Data.py | WFPC2InputImage.find_DQ_extension | def find_DQ_extension(self):
""" Return the suffix for the data quality extension and the name of
the file which that DQ extension should be read from.
"""
dqfile = None
# Look for additional file with DQ array, primarily for WFPC2 data
indx = self._filename.find('.fits... | python | def find_DQ_extension(self):
""" Return the suffix for the data quality extension and the name of
the file which that DQ extension should be read from.
"""
dqfile = None
# Look for additional file with DQ array, primarily for WFPC2 data
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spacetelescope/drizzlepac | drizzlepac/wfpc2Data.py | WFPC2InputImage.setInstrumentParameters | def setInstrumentParameters(self, instrpars):
""" This method overrides the superclass to set default values into
the parameter dictionary, in case empty entries are provided.
"""
pri_header = self._image[0].header
self.proc_unit = instrpars['proc_unit']
instrpars['gn... | python | def setInstrumentParameters(self, instrpars):
""" This method overrides the superclass to set default values into
the parameter dictionary, in case empty entries are provided.
"""
pri_header = self._image[0].header
self.proc_unit = instrpars['proc_unit']
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spacetelescope/drizzlepac | drizzlepac/wfpc2Data.py | WFPC2InputImage.doUnitConversions | def doUnitConversions(self):
""" Apply unit conversions to all the chips, ignoring the group parameter.
This insures that all the chips get the same conversions when this
gets done, even if only 1 chip was specified to be processed.
"""
# Image information
_handl... | python | def doUnitConversions(self):
""" Apply unit conversions to all the chips, ignoring the group parameter.
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# Image information
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spacetelescope/drizzlepac | drizzlepac/wfpc2Data.py | WFPC2InputImage.getdarkcurrent | def getdarkcurrent(self,exten):
"""
Return the dark current for the WFPC2 detector. This value
will be contained within an instrument specific keyword.
The value in the image header will be converted to units
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Returns
-------
darkcurrent : f... | python | def getdarkcurrent(self,exten):
"""
Return the dark current for the WFPC2 detector. This value
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darkcurrent : float
Dark current for the WFPC3 detector... | [
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spacetelescope/drizzlepac | drizzlepac/wfpc2Data.py | WFPC2InputImage.getReadNoise | def getReadNoise(self, exten):
"""
Method for returning the readnoise of a detector (in counts).
Returns
-------
readnoise : float
The readnoise of the detector in **units of counts/electrons**.
"""
rn = self._image[exten]._rdnoise
if self.pr... | python | def getReadNoise(self, exten):
"""
Method for returning the readnoise of a detector (in counts).
Returns
-------
readnoise : float
The readnoise of the detector in **units of counts/electrons**.
"""
rn = self._image[exten]._rdnoise
if self.pr... | [
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readnoise : float
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spacetelescope/drizzlepac | drizzlepac/wfpc2Data.py | WFPC2InputImage.buildMask | def buildMask(self, chip, bits=0, write=False):
""" Build masks as specified in the user parameters found in the
configObj object.
"""
sci_chip = self._image[self.scienceExt,chip]
### For WFPC2 Data, build mask files using:
maskname = sci_chip.dqrootname+'_dqmask.fits... | python | def buildMask(self, chip, bits=0, write=False):
""" Build masks as specified in the user parameters found in the
configObj object.
"""
sci_chip = self._image[self.scienceExt,chip]
### For WFPC2 Data, build mask files using:
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spacetelescope/drizzlepac | drizzlepac/catalogs.py | generateCatalog | def generateCatalog(wcs, mode='automatic', catalog=None,
src_find_filters=None, **kwargs):
""" Function which determines what type of catalog object needs to be
instantiated based on what type of source selection algorithm the user
specified.
Parameters
----------
wcs : obj
... | python | def generateCatalog(wcs, mode='automatic', catalog=None,
src_find_filters=None, **kwargs):
""" Function which determines what type of catalog object needs to be
instantiated based on what type of source selection algorithm the user
specified.
Parameters
----------
wcs : obj
... | [
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catalog : str or ndarray
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spacetelescope/drizzlepac | drizzlepac/catalogs.py | Catalog.generateRaDec | def generateRaDec(self):
""" Convert XY positions into sky coordinates using STWCS methods. """
self.prefix = self.PAR_PREFIX
if not isinstance(self.wcs,pywcs.WCS):
print(
textutil.textbox(
'WCS not a valid PyWCS object. '
'Con... | python | def generateRaDec(self):
""" Convert XY positions into sky coordinates using STWCS methods. """
self.prefix = self.PAR_PREFIX
if not isinstance(self.wcs,pywcs.WCS):
print(
textutil.textbox(
'WCS not a valid PyWCS object. '
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spacetelescope/drizzlepac | drizzlepac/catalogs.py | Catalog.apply_exclusions | def apply_exclusions(self,exclusions):
""" Trim sky catalog to remove any sources within regions specified by
exclusions file.
"""
# parse exclusion file into list of positions and distances
exclusion_coords = tweakutils.parse_exclusions(exclusions)
if exclusion_coord... | python | def apply_exclusions(self,exclusions):
""" Trim sky catalog to remove any sources within regions specified by
exclusions file.
"""
# parse exclusion file into list of positions and distances
exclusion_coords = tweakutils.parse_exclusions(exclusions)
if exclusion_coord... | [
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spacetelescope/drizzlepac | drizzlepac/catalogs.py | Catalog.apply_flux_limits | def apply_flux_limits(self):
""" Apply any user-specified limits on source selection
Limits based on fluxes.
"""
if not self._apply_flux_limits:
return
# only if limits are set should they be applied
if ((self.maxflux is None and self.minflux is None) or... | python | def apply_flux_limits(self):
""" Apply any user-specified limits on source selection
Limits based on fluxes.
"""
if not self._apply_flux_limits:
return
# only if limits are set should they be applied
if ((self.maxflux is None and self.minflux is None) or... | [
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spacetelescope/drizzlepac | drizzlepac/catalogs.py | Catalog.buildCatalogs | def buildCatalogs(self, exclusions=None, **kwargs):
""" Primary interface to build catalogs based on user inputs.
"""
self.generateXY(**kwargs)
self.generateRaDec()
if exclusions:
self.apply_exclusions(exclusions)
# apply selection limits as specified by the ... | python | def buildCatalogs(self, exclusions=None, **kwargs):
""" Primary interface to build catalogs based on user inputs.
"""
self.generateXY(**kwargs)
self.generateRaDec()
if exclusions:
self.apply_exclusions(exclusions)
# apply selection limits as specified by the ... | [
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spacetelescope/drizzlepac | drizzlepac/catalogs.py | Catalog.plotXYCatalog | def plotXYCatalog(self, **kwargs):
"""
Method which displays the original image and overlays the positions
of the detected sources from this image's catalog.
Plotting `kwargs` that can be provided are:
vmin, vmax, cmap, marker
Default colormap is `summer`.
... | python | def plotXYCatalog(self, **kwargs):
"""
Method which displays the original image and overlays the positions
of the detected sources from this image's catalog.
Plotting `kwargs` that can be provided are:
vmin, vmax, cmap, marker
Default colormap is `summer`.
... | [
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spacetelescope/drizzlepac | drizzlepac/catalogs.py | Catalog.writeXYCatalog | def writeXYCatalog(self,filename):
""" Write out the X,Y catalog to a file
"""
if self.xypos is None:
warnstr = textutil.textbox(
'WARNING: \n No X,Y source catalog to write to file. ')
for line in warnstr.split('\n'):
log.warning(line)
... | python | def writeXYCatalog(self,filename):
""" Write out the X,Y catalog to a file
"""
if self.xypos is None:
warnstr = textutil.textbox(
'WARNING: \n No X,Y source catalog to write to file. ')
for line in warnstr.split('\n'):
log.warning(line)
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spacetelescope/drizzlepac | drizzlepac/catalogs.py | ImageCatalog.generateXY | def generateXY(self, **kwargs):
""" Generate source catalog from input image using DAOFIND-style algorithm
"""
#x,y,flux,sharp,round = idlphot.find(array,self.pars['hmin'],self.pars['fwhm'],
# roundlim=self.pars['roundlim'], sharplim=self.pars['sharplim'])
prin... | python | def generateXY(self, **kwargs):
""" Generate source catalog from input image using DAOFIND-style algorithm
"""
#x,y,flux,sharp,round = idlphot.find(array,self.pars['hmin'],self.pars['fwhm'],
# roundlim=self.pars['roundlim'], sharplim=self.pars['sharplim'])
prin... | [
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spacetelescope/drizzlepac | drizzlepac/catalogs.py | UserCatalog.generateXY | def generateXY(self, **kwargs):
"""
Method to interpret input catalog file as columns of positions and fluxes.
"""
self.num_objects = 0
xycols = self._readCatalog()
if xycols is not None:
# convert the catalog into attribute
self.xypos = xycols[:3... | python | def generateXY(self, **kwargs):
"""
Method to interpret input catalog file as columns of positions and fluxes.
"""
self.num_objects = 0
xycols = self._readCatalog()
if xycols is not None:
# convert the catalog into attribute
self.xypos = xycols[:3... | [
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spacetelescope/drizzlepac | drizzlepac/catalogs.py | UserCatalog.plotXYCatalog | def plotXYCatalog(self, **kwargs):
"""
Plots the source catalog positions using matplotlib's `pyplot.plot()`
Plotting `kwargs` that can also be passed include any keywords understood
by matplotlib's `pyplot.plot()` function such as::
vmin, vmax, cmap, marker
"""
... | python | def plotXYCatalog(self, **kwargs):
"""
Plots the source catalog positions using matplotlib's `pyplot.plot()`
Plotting `kwargs` that can also be passed include any keywords understood
by matplotlib's `pyplot.plot()` function such as::
vmin, vmax, cmap, marker
"""
... | [
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