Documentation of functions in toddTools.py

Return to directory of CASA extensions in analysisUtils.py

A broken link here simply means that the command exists and works, but I have not yet written the help page for that command. But there is always inline help available.

          A
  1. accretionEnergy -- Computes gravitational potential energy of a piece of gas falling onto an object
  2. accretionLuminosity -- Computes gravitational potential luminosity of a piece of gas falling toward an object
  3. accretionRadius -- Computes radius required to achieve given accretion rate, central mass, and accretion luminosity
  4. accretionRate -- Computes accretion rate required to achieve accretion luminosity given central mass and radius
  5. addLineToScripts -- Adds a line to the bottom of a script, or list of scripts
  6. addLinks -- Adds soft links to a directory based on existing subdirectory names
  7. adjustDivergingLut -- Removes the middle N values of a diverging RGB color lookup table and stretches the remainder together (to make better outflow palettes)
  8. angularSeparationOfImagePeaks -- Finds the peak in two images and computes the angular separation in arcsec, and fractional beams
  9. aperturePhotometry -- Uses rg.wpolygon to approximate (up to) two circles of different radii, and subtracts the flux of one from the other (works for continuum and cubes)
  10. appendParameterToScript -- Takes a script of N lines containing a call of the same task and appends an additional parameter to the end of each one.
  11. applyRadecOffsetToFile -- Applies an RA/Dec offset to an ASCII table of positions
  12. argmedian -- Returns a list of indices of an array corresponding to the value(s) equal to or closest to the median
  13. atmosphericVariation -- Computes the percentage variation in transmission and Tsky across an image cube's spectral axis
  14. auToRsun -- converts au to solar radii
  15. averageOverIspecs -- Computes the average of two (or more) spectra created by tt.ispec
  16. avgOverCube -- Computes the average spectrum across a multi-dimensional array that has been read from a cube
    B
  17. backgroundSources -- Computes the expected number of background radio point sources in a field
  18. beamAreaRatio -- Computes the ratio of the synthesized beam area between two images
  19. bindingEnergy -- Computes the binding energy of a (uniform density) star of given mass and radius
  20. binge -- Copy a file into multiple other filenames, incrementing a number in the name
  21. blondinEta -- Computes eta parameter from ratio of jet velocity to bowshock velocity
  22. boxToRadians -- Convert a casa region file "box" string to a pair of Ra/Dec's
  23. brightness -- Convert flux density, frequency and beamsize to brightness temperature (and on to dust and gas mass)
  24. brightnesses -- Runs brightness on a list of images
  25. brightnessImage -- Converts an image in flux density units into brightness temperature units
  26. buildAplpyPolygons -- Takes a list of RA/Dec centers and widths/heights/rotations and returns list for show_polygons
  27. buildAplpyRectangles -- Takes a list of RA/Dec centers and widths/heights and returns parameters for show_rectangles
  28. buildBoxRegion -- Builds a casa box region string from the specified blc and trc coordinates (specified in radians)
  29. buildFilterConvolutions -- Add new filters to Robitaille's sedfitter module
  30. buildRobustWeightingGrid -- Run image simulations of all ALMA cycle 5 configurations
  31. buildMomDiff -- builds the images that findContinuum makes: mom0fc, mom8fc, mom0fcScaled and momDiff
    C
  32. calibratorImageFluxes -- Finds the calibrator images of a pipeline runs and reports their fitted flux and noise
  33. calibratorImagePeaks -- Finds the calibrator images of a pipeline runs and reports their peak intesntiy and noise
  34. cardinalShiftRegion -- Reads a polygon region from a CRTF file, shifts it in each of the 4 cardinal directions and writes 4 new CRTF files (up, down, left, right)
  35. carpenterIonizingPhotonRate -- Computes photons/sec for fluxDensity, frequency, distance
  36. cas7210 -- Makes plots for CAS-7210
  37. checkAlternateRefant -- Searches a casa log for appearances of an alternate refant being used in a gain solution
  38. checkBandpassEqualsFlux -- Checks a list of pipeline runs to see if any EB has separate BP and Flux calibrator
  39. checkCalibratorImageFluxes -- Runs au.calibratorImageFluxes on a list of pipeline runs and builds a histogram
  40. checkCompareCparamFromCaltables -- runs compareCparamFromCaltables for a list of pipeline runs
  41. checkCompareTimesFromCaltables -- runs compareTimesFromCaltables for a list of pipeline runs
  42. checkComparePipelineTaskExecutionTimes -- runs comparePipelineTaskExecutionTimes for a list of pipeline runs
  43. checkCorrectMyAntennaPositions -- runs correctMyAntennaPositions for a list of pipeline runs
  44. checkFluxcsv -- runs compareFluxcsv on the flux.csv files from a list of pipeline run pairs
  45. checkForMissingPointingEntries -- Checks a group of pipeline runs for any EB with an antenna with missing pointing table values
  46. checkForMissingPointingSolutions -- Checks a group of pipeline runs for any EB with an antenna with missing pointing calibration solutions
  47. checkForMultipleSolutionTimes -- Checks a collection of pipeline runs for any lowgainflag caltables that contain more than 1 solution time
  48. checkLargeCubeSize -- Computes size in MB of the largest cube per pipeline run of a list of pipeline runs
  49. checkLowgainflag -- Checks a directory of pipeline runs for entries in the text flag tables in the lowgainflag stage
  50. checkLowSNRPositions -- Checks a directory of pipeline runs for low SNR positions rejected by correctMyAntennaPositions
  51. checkLowTransmission -- Looks for low transmission on a per-scan, per-vis basis of a list of pipeline runs
  52. checkLSRKRanges -- runs lsrkRangeForSpw on a list of pipeline runs
  53. checkMultiUserRuns -- Calls checkruns for each specified user in succession
  54. checkNumberOfPhaseCalibrators -- Calls getPhaseCalibrators for a list of pipeline runs
  55. checkNumchan -- Compiles dictionary of number of channels in science spws in a list of pipeline runs
  56. checkOnlineChannelAveraging -- Compiles dictionary of online channel averaging factor in science spws in a list of pipeline runs
  57. checkPads -- Compiles a list of all unique pad names used by a series of pipeline runs
  58. checkPBAtImageCenter -- Calls imageCenter for all continuum images in a series of pipeline runs
  59. checkPipelineBDFlags -- Calls pipelineBDFlags for a list of pipeline runs
  60. checkPipelineChanchunks -- Compiles list of chanchunk values used for mfs and cube imaging in a list of pipeline runs
  61. checkPipelineChecksource -- Checks if a checksource is included in the first EB of each pipeline run in a list of pipeline runs in a directory
  62. checkPipelinePhasecalSolint -- Runs pipelinePhasecalSolint on a list of pipeline runs
  63. checkPipelineRepBWCube -- Searches pipeline working directories for presence of .repBW. cubes
  64. checkPipelineRobust -- Runs pipelineRobust on a set of pipeline runs
  65. checkPipelineSevere -- Runs pipelineSevere on all CASA logs in a set of pipeline runs
  66. checkPipelineSpwBandwidths -- finds the bandwidths of the science spws of a list of pipeline runs
  67. checkPipelineSpwInfo -- runs pipelineSpwInfo for a list of pipeline runs
  68. checkPlotmsMemory -- Runs plotmsMemory on all CASA logs in a set of pipeline runs
  69. checkPlotSpectraFromMask -- Runs plotSpectrumFromMask for all cubes in a set of pipeline runs
  70. checkruns -- Finds the working directory of each pipeline run on the specified root directory
  71. checkStrongTsysLines -- Checks a directory of pipeline runs for the presence of strong features in the Tsys spectra
  72. checkSurmiseConfiguration -- Runs surmiseConfiguration on all ASDMs of a set of pipeline runs
  73. checkTimePipelineImaging -- Builds a dictionary of tclean run times
  74. checkTsysFlags -- Runs pipelineTsysFlag on a set of pipeline runs
  75. checkVersions -- Runs versionsFromWeblog on a list of pipeline runs to compile the CASA and pipeline version info for those project code / MOUS
  76. checkZeroPixels -- Builds a histogram of percentage of pixels equal to zero from a specific 2D image from a series of pipeline runs
  77. clearMask -- clears the mask in a CASA image
  78. clusterCentroid -- Computes the centroid of a set of sky positions, optionally weighted by intensity
  79. clusterMatches -- Computes the nearest neighbor star in list 2 for each star in list 1
  80. clusterStatistics -- Computes statistics of a set of X,Y points or sky positions
  81. collectPipelineSpectra -- Finds all spectra pngs from pipeline images created in a specific pipeline stage
  82. combineMeasurements -- Computes weighted average and standard deviation of several measurements with uncertainties
  83. combineSNRs -- Computes new SNR when combining datasets of a specified SNR
  84. combineUncertainties -- Computes expected new uncertainty when combining datasets
  85. compareFluxcsv -- Compares two flux.csv files
  86. compareFluxcsvs -- Compares a list of pairs of flux.csv files in a directory
  87. compareL80 -- Compares the achieved beamsize in a pipeline reduced dataset with the L80 formula and the im.fitpsf prediction
  88. compareL80list -- Calls compareL80 on a list of pipeline reductions and produces a summary table
  89. composite -- Takes a base png image, and overlays one or two other images on it at a specified offset location and scale size.
  90. computeMeanSeparation -- Compute the mean separation of a set of points
  91. computeRcluster -- Compute the radius and mean position of a set of points.
  92. computeSignedStd -- Compute asymmetric 1-sigma errors of a list
  93. concatSMAdataset -- Uses offsetScanNumbers to concatenate several measurement sets exported from MIR/IDL using autofits and previously filled to ms using MIRSFITStoCASA
  94. convertBenchmarkScript -- Converts a regression script of findContinuum to a new ALMA cycle
  95. convertChannelListIntoSelection -- Converts a list of channels into a CASA selection string syntax, with optional trimming
  96. convertChannelSelectionIntoBandwidthForCube -- Converts a channel list selection for a cube into aggregate bandwidth
  97. convertChannelSelectionIntoFrequencySelectionForCube -- Converts a channel list selection for a cube into frequency list selection
  98. convertChannelSelectionIntoFrequencySelectionForSpw -- Converts a channel list selection for an spw into frequency list selection
  99. convertColonDelimitersToPeriods -- Converts Ra Dec string with colons in the Dec to one with periods in the Dec
  100. convertSelectionIntoChannelList -- Converts a CASA channel selection string into an array of channels.
  101. convolveChannel -- convolves a sinc function with the Hann window, and normalizes the resulting spectrum to unity
  102. convolveChannelAveraging -- convolves a sinc function with the Hann window, then convolves with 2,4,8, or 16 delta functions and normalizes the resulting spectrum to unity
  103. convolveChannelAveragingPlot -- calls convolveChannelAveraging, then plots the result
  104. convolveChannelAveragingPlots -- calls convolveChannelAveragingPlot for each value of 1,2,4,8,16 and builds a montage
  105. convolveChannelPlot -- calls convolveChannel, then plots the result
  106. convolveImfitComponent -- Takes the deconvolved size of an imfit component and convolves it with a different beam
  107. convolveTwoEllipses -- Convolves a gaussian source with the beam of a specified image
  108. correlateRuns -- Compares execution times of two sets of pipeline run pairs
  109. correlateVisstatDifferences -- Computes fractional difference of per-scan/per-spw visibility statistics between two pipeline runs
  110. countLinesPythonCode -- Counts lines of code in *.py files in specified directory tree
  111. crtfMaskSolidAngle -- Computes solid angle of a mask image (such as that built from a crtf file using the CASA task makemask)
  112. crtfSolidAngle -- Computes solid angle of a crtf region
  113. crtfToMask -- Converts a CASA CRTF region file to a mask for a specified image
  114. crtfToPixelList -- Converts a CASA CRTF region file containing 'symbol' shapes to a list of pixels in a specified image
  115. cubeDerivative -- Compute the derivative along the spectral axis of a cube
  116. cubeLSRKRangesToTopo -- Converts an LSRK channel selection string to TOPO frequency ranges and TOPO channel ranges in a specific ms
  117. cumulativeMaserVersusContinuum -- Plots the fraction of maser intensity and spots that are located outside a fractional continuum level in an image
    D
  118. deflection -- Computes the gravitational bending of light for a star at a specified angle for a given distance and mass of a central body
  119. deflectionDifferential -- Computes the differential deflection between two fields in a measurement set
  120. deflectionPlot -- Plots the bending of light vs. angle from the Sun
  121. deflectionPlotJupiter -- Plots the bending of light vs. angle from the Jupiter
  122. deflectionPlotSaturn -- Plots the bending of light vs. angle from the Saturn
  123. deflectionPlotUranus -- Plots the bending of light vs. angle from the Uranus
  124. deflectionPlotNeptune -- Plots the bending of light vs. angle from the Neptune
  125. delaySlope -- Computes change in phase across spw bandwidth for a given delay error
  126. digitizerJitterRequirement -- Computes required jitter for a SNR
  127. digitizerSNR -- Computes SNR for a digitizer with specified number of bits
  128. digitizerSNRjitter -- Computes SNR for a digitizer with specified amount of jitter
  129. dirtyDR -- makes a plot of the dynamic range modifier vs. dynamic range used by the ALMA imaging pipeline
  130. ds9regionToList -- Converts the markers in a ds9 region file from sexagesimal RA, Dec into lists of RA and Dec in degrees
  131. dustLuminosity -- Computes the area under the curve of flux density vs. frequency
  132. dustSublimationRadius -- Computes radius where a power-law temperature profile reaches a specified temperature
  133. dustyProfiles -- Plots radial profiles output by the radiative transfer code DUSTY
  134. dynamicalTime -- Computes dynamical time for an outflow
    E
  135. eddingtonLuminosity -- Computes Eddington limit luminosity for a given mass
  136. editComponentList -- Edits the frequency column in a component list
  137. equivalentAntennas -- Converts sensitivity improvement to equivalent number of antennas added
  138. expandRegion -- Expands a polygonal CASA region file in all directions
  139. exportfits -- Runs exportfits on an image or list of images, automatically appending '.fits'
  140. extractcal -- Extracts all the applycal and gaincal calls from a CASA log and wraps them
  141. extractImagenamesFromScript -- Reads a file of tclean commands and returns a list of the imagename arguments
  142. extractPageFromPDF -- extracts one page from a PDF file
    F
  143. fillFitResults -- Convert output file from Robitaille's sedfitter into easier to read format
  144. filterScriptFor7m -- Filters a list of commands that contain measurement sets, passing only those where the first ms has a majority of 7m antennas"
  145. filterSources -- Extracts a subset of sources within a specified RA/Dec box from a larger list
  146. filterTable -- Filter a list of sources in an ASCII table to those within a specified radius of a specified direction
  147. filtwav -- Extracts the wavelength from a filter defining FITS file in the Robitaille SED fitter package
  148. findChannelRanges -- takes a spectrum and determines a string list of all channel ranges below a threshold
  149. findContinuumCycle8 -- findContinuum for pipeline Cycle 8 (PL2021)
  150. findContinuumForPixel -- Examines the intensity histogram of a spectrum and returns the channels that are close to the continuum level as located by the rolloff point
  151. findContinuumHistogram -- Takes a cube and list of pixels, builds a histogram of flux density to identify continuum level, then finds the best continuum channels (calls findContinuumForPixel or findContinuumForPixelSCL)
  152. findFrequencyForTau -- compute frequency for a specific dust opacity and value of beta
  153. findGreyBodyFluxRatio -- computed the required tau to produce the observed flux ratio between two frequencies
  154. findIntersection -- Finds the intersection point for 2 lines, each defined by a pair of points
  155. findOuterAnnulusForPBCube -- Finds the scaled up values of a size mitigated cube that correspond to 0.2-0.3
  156. findPipelineMeasurementSets -- Finds list of ms in a pipeline run
  157. findSpectralAxis -- finds the spectral axis number of a CASA cube
  158. findTargetFlagVisAndSpw -- finds vislist and spwlist for each vis that contains flags from hifa_targetflag
  159. fitForDustTemp -- Fit for dust temperature, using a measured brightness temperature, source size, and beta
  160. fitForDustTempWithFree -- Fit for free-free component plus a dust temperature, using a measured brightness temperature, source size, and beta
  161. fixEps -- Modifies an eps file with a negative blc bounding box to make it non-negative
  162. fixRestFreq -- Uses imhead to change the restfreq in the header of a cube
  163. flagNonScanTimeRanges -- Flags data by timerange that are outside of the scans of a specified intent
  164. fluxBrightness -- Computes flux density that corresponds to specified brightness temperature
  165. fringeRate -- Computes maximum fringe rate for a specified declination, E-W baseline and frequency
  166. fusOffset -- Applies a frequency shift to an ASCII file spectrum written in the column format expected by CASSIS
  167. fusPlot -- Plots an ASCII file spectrum written in the column format expected by CASSIS
    G
  168. gatherCubeSpectra -- makes a montage of ALMA pipeline cube spectra
  169. gaussianPercentile -- Computes the statistics of a Gaussian distribution restricted to the specified lower percentile
  170. gaussianPercentilePlot -- Plots the statistics of a Gaussian distribution restricted to the specified lower percentile vs. that percentile
  171. getFreqType -- Returns the frequency frame of the specified image
  172. getIntensityForPixel -- Gets the intensity at a specific pixel
  173. getTransitionFrequencies -- Reads a Leiden LAMDA file for a molecule and returns all frequencies
  174. getTransitionInfo -- Reads a Leiden LAMDA file for a molecule and returns 4 lists of info
  175. greybodyFluxDensity -- Computes flux density of a greybody using a dictionary of lmfit parameters
  176. greybodyFluxDensityJy -- Computes flux density of a greybody from temperature, tau, solid angle and frequency
  177. greybodyFluxRatio -- Computes the ratio of flux densities of a greybody at two frequencies
  178. greybodyIntensity -- Computes the intensity of a greybody
    H
  179. help -- prints a list of all the functions defined at the top level of toddTools.py
    I
  180. ifSwingVoltage -- Computes IF swing rms voltage for a specified bandwidth, load resistor, conversion gain and ambient temperature
  181. imageBiweightMean -- Computes the biweight_mean scale of a CASA image using the algorithm in IDLASTRO
  182. imageCompareStats -- Computes the classic and various robust estimators of the rms of a CASA image
  183. imageFromFits -- creates a CASA image from a FITS image that has no RA/Dec coordinates using a template CASA image of the same region
  184. imageFromFORCAST -- creates a CASA image for a SOFIA FORCAST FITS image with 3 planes in the 3rd dimension, using just the first plane
  185. imageRejection -- computes relative integration times as image sideband rejection is improved
  186. imageRobustSigma -- Computes the robust sigma of a CASA image using the algorithm in IDLASTRO
  187. imageSimulationToReality -- Copies a radMC3D simulation cube into the subimage of a cube of the sky
  188. imageSize -- returns size of image in arcseconds or primary beamwidths
  189. imageSizeBytes -- computes the size of all files in a directory tree
  190. imageSpectralIndex -- Computes a spectral index image from two images
  191. imcombine -- Combines non-frequency-overlapping subcubes with the same frequency grid and spatial dimension into a single cube.
  192. imfitBrightnessTemperature -- Reads a list of files of format imfitparseCLB and finds the one with peak intensity, then uses its fitted flux density and fitted size
  193. imfitCube -- Runs imfit on all, or a list of channels in a CASA cube, generating a plot with errorbars
  194. imfitEstimateChanges -- Computes the percentage change in the parameters between two files of imfit estimates
  195. imfitIterate -- Runs imfit successively with the new estimates produced from the previous iteration until the result stops changing
  196. imfitResultsToLatex -- Takes a list of imfit results and produces a Latex table
  197. immoments4panel -- Builds moment images 0,1,2,8 of a CASA cube, then plots them on a 4-panel page
  198. importfitshdu -- imports multiple HDUs from a single FITS image into multiple casa images
  199. importsma -- imports one or more SMA UVFITS files that have been processed by uti_to_topo in MIR IDL
  200. imstatBackground -- run imstat on the specified box region, then on the 4 adjacent boxes to determine the lowest rms in all 5 boxes
  201. imstatCube -- compute the rms and standard deviation of chunks of a CASA image cube, and plots the result
  202. imstatparse -- converts a dictionary returned by imstat into a formatted string
  203. imsubimageRadec -- runs imsubimage centered on a specified RA Dec
  204. imviewOverlayEllipse -- Overlay an ellipse using CASA imview -- obsoleted by au.imviewField(ellipse)
  205. inclinationError -- computes the uncertainty on the inclination of a circular disk based on the apparent major and minor axes of its elliptical projection
  206. insertBookmarks -- insert bookmarks into a PDF
  207. intensityWeightedOffsetToRadec -- combine LL and RR fitted masers into intensity weighted positions nd velocities
  208. invertChannelRanges -- a wrapper function to findChannelRanges which takes just a string and total number of channels (or vis and spw)
  209. ionizingPhotonFlux -- computes equation 1 of Kurtz, Churchwell, Wood (1994)
  210. ionizingPhotonRate -- computes Eq 6 of Turner & Matthews 1984
  211. ionizingPhotonRateFromFluxDensity -- adjusts size of UCHII region until model flux density matches observed
  212. ispec -- Emulates the AIPS task ISPEC to write an ASCII spectrum from one spatial pixel in a cube
  213. ispecOverlay -- Overlay spectrum of a pixel from various cubes
  214. ispecs -- Runs ispec on a list of images
    J
  215. JanskyToFLambda -- Converts flux density to F_lambda in erg cm-2 s-1 um-1
  216. JanskyToLambdaFLambda -- Converts flux density to lambda*F_lambda in erg cm-2 s-1
  217. janskyToKelvinFile -- Converts an ASCII spectrum given in frequency and jansky/beam into frequency and brightness temperature K
  218. kelvinHelmholtzTimescale -- compute this timescale for a specified mass, radius and luminosity
  219. kelvinPerJansky -- computes the Kelvin per Jansky conversion factor for a FITS or CASA interferometric image
  220. keplerianRadius -- given a period and mass (and inclination), returns the radius
  221. keplerianRotation -- given a velocity and radius (and inclination), returns the mass
  222. keplerianVelocity -- given a mass and radius (and inclination), returns the tangential velocity
  223. kurtzIonizingPhotonRate -- Computes photons/sec for electron density, electron temperature and radius
    L
  224. lambdaFLambdaToJansky -- Inverse of janskyToLambdaFLambda (pass an array to get an array)
  225. LbolFromLH2O -- Computes bolometric luminosity from water maser luminosity using Urquhart et al. 2001 Eq 9
  226. lsrkRangeForSpw -- Computes the LSRK frequencies of the first and last channel of the same spw in a list of measurement sets
    M
  227. magjy -- Converts between magnitudes and Janskys for optical through mid-infrared wavelengths
  228. makeFlagTimeRanges -- Builds an array of period timerange strings suitable for use in flagdata on simulated measurement sets
  229. makemaskForNewLine -- Copies the clean mask from one line cube to another
  230. makeMaskFromEstimatesFiles -- Builds an aggregate 2D mask from a list of imfit estimates files using circular apertures
  231. makemaskImage -- Builds a mask image from an existing image and a mask lattice expression
  232. makeNoiseImage -- Takes an image as a template and creates a noise image over the same area
  233. makeNoiseSpectrum -- Makes an array of random numbers of a specified std and mean
  234. makeRobust1cubes -- Builds a script to run tclean to recreate pipeline image cubes with a different robust value
  235. masercloud -- Makes a 3D plot of a sequence of maser spot files
  236. maserLuminosity -- Computes luminosity for a spectral line
  237. maserUpperLimit -- Computes lower limit to the maser increase factor when only upper limits are available from one epoch
  238. maskChannel -- Mask a channel or range of channels in a CASA image cube
  239. meanEpoch -- Uses au.yearFraction to compute mean epoch of a list of dates
  240. meanPosition -- Takes two sexagesimal directions and computes the mean of both axes to produce a new direction
  241. measuredProperMotion -- Takes a measured shift in RA seconds and Dec arcseconds between 2 epochs, and computes proper motion and extrapolates for a third epoch
  242. mergebib -- Takes a .tex and .bbl file and puts the latter into the former, for submission to the ApJL word count tool
  243. minimumMassSolarNebula -- computes mass in Msun for specified surface density, inner and outer radii using a 1/r^2 density profile
  244. minimumSpanningTree -- Computes the minimum spanning tree of a graph
  245. modifySpectrumInCube -- Stuffs a new spectrum of values into a spatial pixel of a CASA image cube
  246. monteCarloAddition -- Computes the joint uncertainty of a sum of measurements with individual uncertainties
  247. monteCarloRatio -- Computes the uncertainty of a measurement scaled by an uncertain scale factor
    N
  248. nanmean -- Returns scipy.stats.nanmean if numpy is earlier than 1.81, otherwise returns np.nanmean
  249. nanmedian -- Returns scipy.stats.nanmedian if numpy is earlier than 1.81, otherwise returns np.nanmedian
  250. nearestSourceInFitsTable -- Finds the nearest source in a FITS table to a specified direction
  251. nextPowerOfTwo -- Computes the next power of 2 greater than or equal to the specified integer
  252. nonScanTimeRanges -- Returns a list of date/time ranges outside of the scans of a specified intent
  253. northalign -- Uses the montage python wrapper to align a FITS image to north up
    O
  254. offsetScanNumbers -- Adds a constant to the SCAN_NUMBER column of a measurement set
  255. olnon -- Computes free-free spectral energy distribution from the models of Olnon 1975
  256. oneEvent -- For a given population size, compute the sigma that gives just one event
  257. outburstEnergy -- Computes Joules in a protostellar outburst from luminosity and years
  258. outermosaic -- Computes the border points of a mosaic pointing pattern
    P
  259. phaseScreenCorrupt -- Corrupts a measurement set using the sm.settrop method.
  260. photonStep -- Compute photon step for a specified frequency
  261. pipelineBandpassTimeSolint -- Searches CASA log for longest time solint on bandpass calibartor
  262. pipelineBeamRadius -- Emulates the calculation in imageparams_base.py
  263. pipelineMeanVisibility -- Extracted code from gcorfluxscale.py
  264. pipelinePhasecalSolint -- Checks for solint specified gaincal as a value in 's'econds, rather than 'int' or 'inf'
  265. pipelinePlottingTimes -- Computes time spent in making sky plots in hif_makeimages
  266. pipelineSpwphaseupSpwmap -- finds the spwmap used by the pipeline in spwhpaseup
  267. pipelineSpwBandwidths -- finds the bandwidths of the science spws of a pipeline run's MOUS
  268. pipelineSpwInfo -- Reports a dictionary of science spws for a pipelien run with values of nChannels and bandwidth
  269. pipelineSpwNChannels -- Reports number of channels per science spw in a pipeline run
  270. pipe337beforeAfter -- Makes before/after plots for the hifa_targetflag flags
  271. planckIntensity -- Computes the intensity of the Planck function
  272. plotAplpyLines -- Plots a list of line segments from an ASCII file onto an aplpy figure
  273. plotAplpyPositionAngle -- Plots a line along a position angle on an aplpy FitsFigure
  274. plotCalibratorImagePeaks -- Plots an SED of the image peaks of the per-spw calibrator continuum images
  275. plotCompareFluxcsvs -- Plots age of spectral index vs. separationWindow, from several runs of compareFluxcsvs
  276. plotCompareL80 -- Plots the results from compareL80list
  277. plotFluxMaxAge -- Plots the SSR-generated file used by the OT in ICT-13764
  278. plotHartRAO -- Plots maser spectra ascii files from HartRAO
  279. plotHartRAODifference -- Plots the difference between two maser spectra ascii files from HartRAO
  280. plotLinesOfCodeVsTime -- Plots the lines of code vs. cvs version number and vs. time
  281. plotMaxHoldSpectrum -- Plots the maximum of a uv spectrum output by plotms text file tool
  282. plotRegionSpectrum -- computes and plots the spectrum from the unmasked pixels in a CASA region file
  283. plotRobustGrid -- Plots the results file from buildRobustWeightingGrid
  284. plotSMAEngineeringData -- plots data files downloaded from http://sma1.sma.hawaii.edu/internal/plot/customplots.html
  285. plotSpwsVsTime -- Plots the science spws that appear in scans vs. time (or scan ID)
  286. plotTimePipelineImaging -- Makes histograms from a dictionary created by checkTimePipelineImaging
  287. plotTLEazel -- plots a satellite azimuth, elevation file produce by SxP4Test
  288. polarizationUncertainty -- computes polarization percentage and its uncertainty from I, Q, U flux densities and image rms
  289. properMotion -- computes proper motion in mas/year and beams/year for a specified distance, velocity and antenna configuration
  290. propertiesForIonizingPhotonRateDiazMiller -- determine interpolated ZAMS stellar properties for the specified value of Lyman continuum photon rate
  291. propertiesForSpectralTypeHanson -- determine interpolated ZAMS stellar properties for the specified spectral type
  292. pruneMask -- Calls Tak's prune algorithm used by tclean autoboxing
    Q
  293. quantizationCorrection -- Formulas 8.67 and 8.68 of TMS using optimal values of level separation (epsilon) from Thompson, Emerson and Schwab (2007)
  294. quantumLimit -- Computes quantum limited Trx values for a given frequency
    R
  295. radecListToOffsets -- Converts a list of sexagesimal RA/Dec values into relative coordinates in arcsec (relative to first position in the list)
  296. readPolygonRegion -- Reads a polygon shape from a CRTF file
  297. regionSpectrum -- Computes the spectrum from a specified region of a CASA image
  298. regionToEstimates -- Converts a CASA region file of positions to a imfit estimates file
  299. relaxationTime -- Computes relaxation time of a stellar cluster
  300. removeNaNs -- remove (or replace) the NaNs from an array
  301. removeLastLineOfFile -- removes the final line of an ASCII file, or list of files
  302. removeLines -- removes all lines of an ASCII file that contain a specified string (used for culling AQUA/QA0 bugs in flag command txt files)
  303. replaceMaskedPixels -- replaces masked pixels in a CASA image with a specified value
  304. replaceStringInFiles -- replaces a string with another string in a list of files
  305. robitailleLuminosity -- integrates the lambda*F_lambda SED of a Robitaille model to compute apparment luminosity
  306. robitailleStefanBoltzmann -- reads a text file of best fitting Robitaille models and computes luminosity of protostar from Teff and radius
  307. rotationPhase -- determines the rotational phase of an observation relative to a zero point in the past
    S
  308. roundMeasurementToAsymmetricString -- converts a value and uncertainty to a latex string with different + and - error bars
  309. roundMeasurementToAsymmetricScientificString -- converts a value and uncertainty to a latex string in scientific notation with different + and - error bars
  310. roundMeasurementToScientificString -- converts a value and uncertainty to a latex string in scientific notation
  311. roundMeasurementToString -- converts a value and uncertainty to a string
  312. scaleFluxcsv -- Scales the flux densities in an ALMA pipeline's flux.csv file
  313. scaleImage -- Scales the intensity in one or more rectangular boxes in a CASA image by a scale factor
  314. scaleImageSize -- Takes a string like '100x60' and scales each number by a specified factor
  315. scanTimeRanges -- Returns a list of date/time ranges for all the scans of a specified intent
  316. shadowedArea -- Computes percentage of antenna area shadowed for a given linear overlap
  317. shiftDecString -- Takes a sexagesimal format Dec Value and shifts it by a specified value of arcseconds
  318. shiftPolygonRegion -- Reads a polygon region from a CRTF file, shifts it a specified amount and writes a new CRTF file
  319. shiftRAString -- Takes a sexagesimal format RA value and shifts it by a specified value of arcseconds
  320. shortenCasalog -- Removes all messages from CASA tasks (helpful when debugging non-tasks)
  321. show_circles_intersecting -- Implements aplpy's show_circles but prevents drawing portions that overlap other circles.
  322. sigmaEvent -- compute the probability of an N-sigma event
  323. sisLOPowerRequirement -- Compute LO power required for a specified frequency, junction resistance and coupling factor
  324. sisOptimalImpedance -- Compute optimal impedance for an SIS mixer tuning circuit
  325. specfitPlot -- Plots the fit result from the CASA task specfit
  326. spectralTypeFloatToStringTo -- converts 0.95 to 'O9.5' for use after interpolating tables
  327. spectralTypeSternberg -- returns spectral type and luminosity for Q value for class V stars
  328. spectralTypeStringToFloat -- converts 'O9.5' to 0.95 for use in interpolating tables
  329. spectralTypeToTemperature -- uses Pecaut & Mamajek 2013 to convert spectral type to surface temperature
  330. spectraOverlay -- Reads and plots a spectral profile ASCII file created by the CASA viewer
  331. splitSedResults -- Split an sed_results file into N files to prepare it for Robitaille's fitter
  332. stefanBoltzmannLuminosity -- convert radius, distance and temperature to luminosity
  333. stefanBoltzmannRadius -- convert luminosity and temperature to radius
  334. stefanBoltzmannTemperature -- convert luminosity and radius to temperature
  335. stringToURL -- convert a text string to an encoded version suitable for use in a URL
    T
  336. tauFromBrightness -- Inverts the equation Tb = T*(1-exp(-tau))
  337. temperatureToSpectralType -- interpolates Table 5 of Pecaut & Mamajek 2013
  338. timegaincalInterval -- Reads the bandpass/flux phase-only solint from the timegaincal weblog table
  339. topoFreqToChannel -- Converts a list of topo frequencies to topo channels in a measurement set
  340. topoFreqRangeListToChannel -- Converts a semicolon-delimit list of frequency ranges to topo channel ranges
  341. toutZAMS -- Computes radius, luminosity and temperature for a ZAMS star as a function of mass and metallicity
  342. truncatedJDToDatestring -- converts truncated JD to date string
  343. tskyGridPlot -- makes a grid of plots of Tsky vs. frequency from a list of measurement sets and maxAltitudes
    V
  344. uncertaintyOfSummedValues -- computes uncertainty of a sum of measurements
    V
  345. velocityChannelWidth -- Returns the width of cube channels in velocity units
  346. version -- returns the CVS version number of toddTools.py
  347. visibleSky -- compute the fraction of the sky ever visible from a specified latitude and horizon limit
  348. vislistFromFluxcsv -- Returns list of measurement sets contained a flux.csv file
    W
  349. widthOfMaskArcsec -- Finds the width of the smallest central square that circumscribes a mask
    Z
  350. zams -- Computes luminosity and radius for a given stellar mass using Hosokawa's fits to Schaller et al. 1992
  351. zamsMassFromLuminosity -- Computes empirical relation of Demircan and Kahraman 1991
  352. zeeman -- fits Stokes I and V spectra for Zeeman effect and magnetic field
-- ToddHunter - 2014-08-13
Topic revision: r198 - 2021-12-01, ToddHunter
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