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.

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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. antennaCombinations -- Computes the number of N-antenna subsets of the specified array size
10. antennaVelocityDifference -- Computes maximum differential velocity of Earth rotation for a given east-west baseline and latitude
11. 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)
12. 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.
13. applyRadecOffsetToFile -- Applies an RA/Dec offset to an ASCII table of positions
14. argmedian -- Returns a list of indices of an array corresponding to the value(s) equal to or closest to the median

1. atacCombinations -- Computes the fraction of 4-antenna combinations possible in the ATAC.HILSE if each fully-populated AVCC can select 1 of its 4 attached antennas
2. atmosphericVariation -- Computes the percentage variation in transmission and Tsky across an image cube's spectral axis
3. auToRsun -- converts au to solar radii
4. averageOverIspecs -- Computes the average of two (or more) spectra created by tt.ispec
5. avgOverCube -- Computes the average spectrum across a multi-dimensional array that has been read from a cube
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6. backgroundSources -- Computes the expected number of background radio point sources in a field
7. beamAreaRatio -- Computes the ratio of the synthesized beam area between two images
8. bindingEnergy -- Computes the binding energy of a (uniform density) star of given mass and radius
9. binge -- Copy a file into multiple other filenames, incrementing a number in the name
10. blondinEta -- Computes eta parameter from ratio of jet velocity to bowshock velocity
11. boxToRadians -- Convert a casa region file "box" string to a pair of Ra/Dec's
12. brightness -- Convert flux density, frequency and beamsize to brightness temperature (and on to dust and gas mass)
13. brightnesses -- Runs brightness on a list of images
14. brightnessImage -- Converts an image in flux density units into brightness temperature units
15. buildAplpyPolygons -- Takes a list of RA/Dec centers and widths/heights/rotations and returns list for show_polygons
16. buildAplpyRectangles -- Takes a list of RA/Dec centers and widths/heights and returns parameters for show_rectangles
17. buildBoxRegion -- Builds a casa box region string from the specified blc and trc coordinates (specified in radians)
18. buildDecimatedCubes -- Decimates in RA and Dec the findcont .residual and .psf cubes from a directory of pipeline runs
19. buildFilterConvolutions -- Add new filters to Robitaille's sedfitter module
20. buildRobustWeightingGrid -- Run image simulations of all ALMA cycle 5 configurations
21. buildMomDiff -- builds the images that findContinuum makes: mom0fc, mom8fc, mom0fcScaled and momDiff
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22. calibratorImageFluxes -- Finds the calibrator images of a pipeline runs and reports their fitted flux and noise
23. calibratorImagePeaks -- Finds the calibrator images of a pipeline runs and reports their peak intesntiy and noise
24. callenWeltonNoise -- Computes Equation 6 of ALMA memo 161
25. 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)
26. carpenterIonizingPhotonRate -- Computes photons/sec for fluxDensity, frequency, distance
27. cas7210 -- Makes plots for CAS-7210
28. checkAlternateRefant -- Searches a casa log for appearances of an alternate refant being used in a gain solution
29. checkBandpassEqualsFlux -- Checks a list of pipeline runs to see if any EB has separate BP and Flux calibrator
30. checkCalibratorImageFluxes -- Runs au.calibratorImageFluxes on a list of pipeline runs and builds a histogram
31. checkCompareCparamFromCaltables -- runs compareCparamFromCaltables for a list of pipeline runs
32. checkCompareTimesFromCaltables -- runs compareTimesFromCaltables for a list of pipeline runs
33. checkComparePipelineTaskExecutionTimes -- runs comparePipelineTaskExecutionTimes for a list of pipeline runs
34. checkCorrectMyAntennaPositions -- runs correctMyAntennaPositions for a list of pipeline runs
35. checkCycleTime -- runs cycleTime for the first EB of each pipeline run in a directory of pipeline runs
36. checkDurationOfBandpassScans -- runs computeDurationOfScans for first EB of each pipeline run in a directory of pipeline runs
37. checkFluxcsv -- runs compareFluxcsv on the flux.csv files from a list of pipeline run pairs
38. checkForMissingPointingEntries -- Checks a group of pipeline runs for any EB with an antenna with missing pointing table values
39. checkForMissingPointingSolutions -- Checks a group of pipeline runs for any EB with an antenna with missing pointing calibration solutions
40. checkForMultipleSolutionTimes -- Checks a collection of pipeline runs for any lowgainflag caltables that contain more than 1 solution time
41. checkLargeCubeSize -- Computes size in MB of the largest cube per pipeline run of a list of pipeline runs
42. checkLowgainflag -- Checks a directory of pipeline runs for entries in the text flag tables in the lowgainflag stage
43. checkLowSNRPositions -- Checks a directory of pipeline runs for low SNR positions rejected by correctMyAntennaPositions
44. checkLowTransmission -- Looks for low transmission on a per-scan, per-vis basis of a list of pipeline runs
45. checkLSRKRanges -- runs lsrkRangeForSpw on a list of pipeline runs
46. checkMosaicTimeGapBetweenFields -- runs mosaicTimeGapBetweenFields for the first EB of each pipeline run in a directory of pipeline runs
47. checkMultiUserRuns -- Calls checkruns for each specified user in succession
48. checkNallcontCubes -- Runs findPipelineAllcontCubes on a directory of pipeline runs
49. checkNantennas -- Compiles dictionary of number of antennas in first EB of a directory of pipeline runs
50. checkNumberOfPhaseCalibrators -- Calls getPhaseCalibrators for a list of pipeline runs
51. checkNumchan -- Compiles dictionary of number of channels in science spws in a list of pipeline runs
52. checkOnlineChannelAveraging -- Compiles dictionary of online channel averaging factor in science spws in a list of pipeline runs
53. checkPads -- Compiles a list of all unique pad names used by a series of pipeline runs
54. checkPBAtImageCenter -- Calls imageCenter for all continuum images in a series of pipeline runs
55. checkPipelineBDFlags -- Calls pipelineBDFlags for a list of pipeline runs
56. checkPipelineChanchunks -- Compiles list of chanchunk values used for mfs and cube imaging in a list of pipeline runs
57. checkPipelineChecksource -- Checks if a checksource is included in the first EB of each pipeline run in a list of pipeline runs in a directory
58. checkPipelineFieldnames -- Checks if any pipeline image cube names contain integer field names and returns a dictionary of them
59. checkPipelineIntegrationTimes -- Returns a dictionary keyed by intent with values being the integration time in the first vis, and a Boolean on whether they differ
60. checkPipelinePhasecalSolint -- Runs pipelinePhasecalSolint on a list of pipeline runs
61. checkPipelinePlotmsMPIFraction -- Returns a dictionary keyed by project_MOUS, with 3 values: parallel, total, fraction
62. checkPipelinePlotmsMPIFractionHistogram -- Builds a histogram from the results of checkPipelinePlotmsMPIFraction
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. checkPipelineSingleEBMOUS -- Returns a list of strings of format 'projectCode,MOUS,workingdir' for pipeline runs that contain only a single EB
67. checkPipelineSpwBandwidths -- finds the bandwidths of the science spws of a list of pipeline runs
68. checkPipelineSpwInfo -- runs pipelineSpwInfo for a list of pipeline runs
69. checkPlotmsMemory -- Runs plotmsMemory on all CASA logs in a set of pipeline runs
70. checkPlotSpectraFromMask -- Runs plotSpectrumFromMask for all cubes in a set of pipeline runs
71. checkruns -- Finds the working directory of each pipeline run on the specified root directory
72. checkStrongTsysLines -- Checks a directory of pipeline runs for the presence of strong features in the Tsys spectra
73. checkSurmiseConfiguration -- Runs surmiseConfiguration on all ASDMs of a set of pipeline runs
74. checkTimePipelineImaging -- Builds a dictionary of tclean run times
75. checkTsysFlags -- Runs pipelineTsysFlag on a set of pipeline runs
76. checkUVspectra -- Takes output of checkPipelineSingleEBMOUS (a list of vis from pipeline runs with only 1 EB) and runs au.uvspectrum on each one
77. checkVersions -- Runs versionsFromWeblog on a list of pipeline runs to compile the CASA and pipeline version info for those project code / MOUS
78. checkZeroPixels -- Builds a histogram of percentage of pixels equal to zero from a specific 2D image from a series of pipeline runs
79. clearMask -- clears the mask in a CASA image
80. clusterCentroid -- Computes the centroid of a set of sky positions, optionally weighted by intensity
81. clusterMatches -- Computes the nearest neighbor star in list 2 for each star in list 1
82. clusterStatistics -- Computes statistics of a set of X,Y points or sky positions
83. collectPipelineSpectra -- Finds all spectra pngs from pipeline images created in a specific pipeline stage
84. combinationsOf4 -- Computes the percentage of 4-antenna subsets that have independent fiber optic transceiver colors
85. combineMeasurements -- Computes weighted average and standard deviation of several measurements with uncertainties
86. combineSNRs -- Computes new SNR when combining datasets of a specified SNR
87. combineUncertainties -- Computes expected new uncertainty when combining datasets
88. compareFluxcsv -- Compares two flux.csv files
89. compareFluxcsvs -- Compares a list of pairs of flux.csv files in a directory
90. compareL80 -- Compares the achieved beamsize in a pipeline reduced dataset with the L80 formula and the im.fitpsf prediction
91. compareL80list -- Calls compareL80 on a list of pipeline reductions and produces a summary table
92. compareStats -- Compares two dictionaries from visstat stored in plain text files (for PIPE-1776)
93. composite -- Takes a base png image, and overlays one or two other images on it at a specified offset location and scale size.
94. computeDelayRate -- computes delay rate in ns/sec for a specified rate in units of sidereal rate
95. computeMeanSeparation -- Compute the mean separation of a set of points
96. computeMom0peakOverMad -- Computes the ratio of the imstat 'max' over 'medabsdevmed' of a specified image
97. computeRcluster -- Compute the radius and mean position of a sehttpdrt://science.nrao.edu/facilities/alma/science_sustainability/na-alma-develpment-fy2023-call-for-study-proposalst of points.
98. computeSignedStd -- Compute asymmetric 1-sigma errors of a list
99. concatSMAdataset -- Uses offsetScanNumbers to concatenate several measurement sets exported from MIR/IDL using autofits and previously filled to ms using MIRSFITStoCASA
100. constellation -- Calls astropy's get_constellation for a specified RA/Dec
101. convertBenchmarkScript -- Converts a regression script of findContinuum to a new ALMA cycle
102. convertChannelListIntoSelection -- Converts a list of channels into a CASA selection string syntax, with optional trimming
103. convertChannelSelectionIntoBandwidthForCube -- Converts a channel list selection for a cube into aggregate bandwidth
104. convertChannelSelectionIntoChannelSelection -- convert channel selection from one cube into another cube (with a different channelization)
105. convertChannelSelectionIntoFrequencySelectionForCube -- Converts a channel list selection for a cube into frequency list selection
106. convertChannelSelectionIntoFrequencySelectionForSpw -- Converts a channel list selection for an spw into frequency list selection
107. convertColonDelimitersToPeriods -- Converts Ra Dec string with colons in the Dec to one with periods in the Dec
108. convertSainiCSVFilesToFEICsquintFormat -- Converts per-Band .csv files dumped from per-Band .xls files created by Christopher at CDL (for Saini) into a single multi-Band csv file compatible with the original NA FEIC csv file
109. convertSelectionIntoChannelList -- Converts a CASA channel selection string into an array of channels.
110. convolveChannel -- convolves a sinc function with the Hann window, and normalizes the resulting spectrum to unity
111. 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
112. convolveChannelAveragingPlot -- calls convolveChannelAveraging, then plots the result
113. convolveChannelAveragingPlots -- calls convolveChannelAveragingPlot for each value of 1,2,4,8,16 and builds a montage
114. convolveChannelPlot -- calls convolveChannel, then plots the result
115. convolveImfitComponent -- Takes the deconvolved size of an imfit component and convolves it with a different beam
116. convolveTwoEllipses -- Convolves a gaussian source with the beam of a specified image
117. cornersMaskedButEdgesNotMasked -- returns True if the 4 corner pixels are masked but the 4 edge pixels are not
118. correctionsForRandomGauss --Computes corrections for the median and MAD of a population as judged by a sample from one end of the percentile distribution (developed for findContinuum)
119. correlateRuns -- Compares execution times of two sets of pipeline run pairs
120. correlateVisstatDifferences -- Computes fractional difference of per-scan/per-spw visibility statistics between two pipeline runs
121. countLinesPythonCode -- Counts lines of code in *.py files in specified directory tree
122. crtfMaskSolidAngle -- Computes solid angle of a mask image (such as that built from a crtf file using the CASA task makemask)
123. crtfSolidAngle -- Computes solid angle of a crtf region
124. crtfToMask -- Converts a CASA CRTF region file to a mask for a specified image
125. crtfToPixelList -- Converts a CASA CRTF region file containing 'symbol' shapes to a list of pixels in a specified image
126. cryostatTemperaturePlot -- Reads a file downloaded from TMCDB with au.getCryostatTemperaturesFromTMCDB and generates a histogram
127. cryostatTemperaturePlots -- Runs cryostatTemperaturePlot for a list of bands and sensors and builds a PDF of the resulting histograms.
128. cubeDerivative -- Compute the derivative along the spectral axis of a cube
129. cubeLSRKRangesToTopo -- Converts an LSRK channel selection string to TOPO frequency ranges and TOPO channel ranges in a specific ms
130. cumulativeMaserVersusContinuum -- Plots the fraction of maser intensity and spots that are located outside a fractional continuum level in an image
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131. deflection -- Computes the gravitational bending of light for a star at a specified angle for a given distance and mass of a central body
132. deflectionDifferential -- Computes the differential deflection between two fields in a measurement set
133. deflectionPlot -- Plots the bending of light vs. angle from the Sun
134. deflectionPlotJupiter -- Plots the bending of light vs. angle from the Jupiter
135. deflectionPlotSaturn -- Plots the bending of light vs. angle from the Saturn
136. deflectionPlotUranus -- Plots the bending of light vs. angle from the Uranus
137. deflectionPlotNeptune -- Plots the bending of light vs. angle from the Neptune
138. delayLoss -- Compute loss of SNR due to an rms delay error
139. delaySlope -- Computes change in phase across spw bandwidth for a given delay error
140. digitizerJitterRequirement -- Computes required jitter for a SNR
141. digitizerSNR -- Computes SNR for a digitizer with specified number of bits
142. digitizerSNRjitter -- Computes SNR for a digitizer with specified amount of jitter
143. digitizeSignal -- Converts a real-valued signal into a discrete level signal
144. dirtyDR -- makes a plot of the dynamic range modifier vs. dynamic range used by the ALMA imaging pipeline
145. ds9regionToList -- Converts the markers in a ds9 region file from sexagesimal RA, Dec into lists of RA and Dec in degrees
146. dustLuminosity -- Computes the area under the curve of flux density vs. frequency
147. dustSublimationRadius -- Computes radius where a power-law temperature profile reaches a specified temperature
148. dustyProfiles -- Plots radial profiles output by the radiative transfer code DUSTY
149. dynamicalTime -- Computes dynamical time for an outflow
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150. earthRotationSpeed -- Computes rotation speed at surface of earth for a given latitude
151. eddingtonLuminosity -- Computes Eddington limit luminosity for a given mass
152. editComponentList -- Edits the frequency column in a component list
153. equivalentAntennas -- Converts sensitivity improvement to equivalent number of antennas added
154. expandRegion -- Expands a polygonal CASA region file in all directions
155. exponentialDecayFit -- Fits the logarithm of y vs. linear x (in years), computing e-folding time (in days)
156. exportfits -- Runs exportfits on an image or list of images, automatically appending '.fits'
157. extractcal -- Extracts all the applycal and gaincal calls from a CASA log and wraps them
158. extractImagenamesFromScript -- Reads a file of tclean commands and returns a list of the imagename arguments
159. extractPageFromPDF -- extracts one page from a PDF file
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160. fiberLengthHistogram -- plots a histogram of the 192 antenna pad to AOS TB fiber lengths
161. fillFitResults -- Convert output file from Robitaille's sedfitter into easier to read format
162. filterScriptFor7m -- Filters a list of commands that contain measurement sets, passing only those where the first ms has a majority of 7m antennas"
163. filterSources -- Extracts a subset of sources within a specified RA/Dec box from a larger list
164. filterTable -- Filter a list of sources in an ASCII table to those within a specified radius of a specified direction
165. filtwav -- Extracts the wavelength from a filter defining FITS file in the Robitaille SED fitter package
166. findChannelRanges -- takes a spectrum and determines a string list of all channel ranges below a threshold
167. findContinuumCycle8 -- findContinuum for pipeline Cycle 8 (PL2021)
168. 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
169. 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)
170. findFrequencyForTau -- compute frequency for a specific dust opacity and value of beta
171. findGreyBodyFluxRatio -- computed the required tau to produce the observed flux ratio between two frequencies
172. findIntersection -- Finds the intersection point for 2 lines, each defined by a pair of points
173. findOuterAnnulusForPBCube -- Finds the scaled up values of a size mitigated cube that correspond to 0.2-0.3
174. findPipelineMeasurementSets -- Finds list of ms in a pipeline run
175. findSpectralAxis -- finds the spectral axis number of a CASA cube
176. findTargetFlagVisAndSpw -- finds vislist and spwlist for each vis that contains flags from hifa_targetflag
177. fitForDustTemp -- Fit for dust temperature, using a measured brightness temperature, source size, and beta
178. fitForDustTempWithFree -- Fit for free-free component plus a dust temperature, using a measured brightness temperature, source size, and beta
179. fixEps -- Modifies an eps file with a negative blc bounding box to make it non-negative
180. fixRestFreq -- Uses imhead to change the restfreq in the header of a cube
181. flagNonScanTimeRanges -- Flags data by timerange that are outside of the scans of a specified intent
182. flipEstimatesFiles -- For 2-component imfit estimates files, exchange the spread of RA and Dec
183. fluxBrightness -- Computes flux density that corresponds to specified brightness temperature
184. fringeRate -- Computes maximum fringe rate for a specified declination, E-W baseline and frequency
185. fusOffset -- Applies a frequency shift to an ASCII file spectrum written in the column format expected by CASSIS
186. fusPlot -- Plots an ASCII file spectrum written in the column format expected by CASSIS
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187. g358bayandinaBrogan -- converts Table 4 of Bayandina, Brogan, et al. 2022 into aplpy-friendly files
188. g358ellipse --
189. g358pcygni -- runs ispecPlot overlay of 3 spectra
190. g358sed --
191. gatherCubeSpectra -- makes a montage of ALMA pipeline cube spectra
192. gaussianPercentile -- Computes the statistics of a Gaussian distribution restricted to the specified lower percentile
193. gaussianPercentilePlot -- Plots the statistics of a Gaussian distribution restricted to the specified lower percentile vs. that percentile
194. getFreqType -- Returns the frequency frame of the specified image
195. getIntensityForPixel -- Gets the intensity at a specific pixel
196. getTransitionFrequencies -- Reads a Leiden LAMDA file for a molecule and returns all frequencies
197. getTransitionInfo -- Reads a Leiden LAMDA file for a molecule and returns 4 lists of info
198. greybodyFluxDensity -- Computes flux density of a greybody using a dictionary of lmfit parameters
199. greybodyFluxDensityJy -- Computes flux density of a greybody from temperature, tau, solid angle and frequency
200. greybodyFluxRatio -- Computes the ratio of flux densities of a greybody at two frequencies
201. greybodyIntensity -- Computes the intensity of a greybody
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202. help -- prints a list of all the functions defined at the top level of toddTools.py
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203. ifSwingVoltage -- Computes IF swing rms voltage for a specified bandwidth, load resistor, conversion gain and ambient temperature
204. imageBiweightMean -- Computes the biweight_mean scale of a CASA image using the algorithm in IDLASTRO
205. imageCompareStats -- Computes the classic and various robust estimators of the rms of a CASA image
206. imageDynamicRange -- Encodes equation of Perley 1999 / Braun 2013
207. imageFromFits -- creates a CASA image from a FITS image that has no RA/Dec coordinates using a template CASA image of the same region
208. imageFromFORCAST -- creates a CASA image for a SOFIA FORCAST FITS image with 3 planes in the 3rd dimension, using just the first plane
209. imageRobustSigma -- Computes the robust sigma of a CASA image using the algorithm in IDLASTRO
210. imageSimulationToReality -- Copies a radMC3D simulation cube into the subimage of a cube of the sky
211. imageSize -- returns size of image in arcseconds or primary beamwidths
212. imageSizeBytes -- computes the size of all files in a directory tree
213. imageSpectralIndex -- Computes a spectral index image from two images
214. imcombine -- Combines non-frequency-overlapping subcubes with the same frequency grid and spatial dimension into a single cube.
215. 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
216. imfitCube -- Runs imfit on all, or a list of channels in a CASA cube, generating a plot with errorbars
217. imfitEstimateChanges -- Computes the percentage change in the parameters between two files of imfit estimates
218. imfitIterate -- Runs imfit successively with the new estimates produced from the previous iteration until the result stops changing
219. imfitResultsToLatex -- Takes a list of imfit results and produces a Latex table
220. immoments4panel -- Builds moment images 0,1,2,8 of a CASA cube, then plots them on a 4-panel page
221. importfitshdu -- imports multiple HDUs from a single FITS image into multiple casa images
222. importsma -- imports one or more SMA UVFITS files that have been processed by uti_to_topo in MIR IDL
223. imstatBackground -- run imstat on the specified box region, then on the 4 adjacent boxes to determine the lowest rms in all 5 boxes
224. imstatCube -- compute the rms and standard deviation of chunks of a CASA image cube, and plots the result
225. imstatparse -- converts a dictionary returned by imstat into a formatted string
226. imsubimageRadec -- runs imsubimage centered on a specified RA Dec
227. imviewOverlayEllipse -- Overlay an ellipse using CASA imview -- obsoleted by au.imviewField(ellipse)
228. inclinationError -- computes the uncertainty on the inclination of a circular disk based on the apparent major and minor axes of its elliptical projection
229. insertBookmarks -- insert bookmarks into a PDF
230. intensityProfile -- extracts and plots intensity profile from a single plane image (2D, 3D, or 4D) or the on-the-fly-channel-average of a cube
231. intensityWeightedOffsetToRadec -- combine LL and RR fitted masers into intensity weighted positions nd velocities
232. interpolateEpsilon -- interpolates the optimal level spacing for non-power-of-2 quantization levels
233. invertChannelRanges -- a wrapper function to findChannelRanges which takes just a string and total number of channels (or vis and spw)
234. ionizingPhotonFlux -- computes equation 1 of Kurtz, Churchwell, Wood (1994)
235. ionizingPhotonRate -- computes Eq 6 of Turner & Matthews 1984
236. ionizingPhotonRateFromFluxDensity -- adjusts size of UCHII region until model flux density matches observed
237. ispec -- Emulates the AIPS task ISPEC to write an ASCII spectrum from one spatial pixel in a cube
238. ispecOverlay -- Overlay spectrum of a pixel from various cubes
239. ispecs -- Runs ispec on a list of images
     J
240. JanskyToFLambda -- Converts flux density to F_lambda in erg cm-2 s-1 um-1
241. JanskyToLambdaFLambda -- Converts flux density to lambda*F_lambda in erg cm-2 s-1
242. janskyToKelvinFile -- Converts an ASCII spectrum given in frequency and jansky/beam into frequency and brightness temperature K
243. kelvinHelmholtzTimescale -- compute this timescale for a specified mass, radius and luminosity
244. kelvinPerJansky -- computes the Kelvin per Jansky conversion factor for a FITS or CASA interferometric image
245. keplerianRadius -- given a period and mass (and inclination), returns the radius
246. keplerianRotation -- given a velocity and radius (and inclination), returns the mass
247. keplerianVelocity -- given a mass and radius (and inclination), returns the tangential velocity
248. kurtzIonizingPhotonRate -- Computes photons/sec for electron density, electron temperature and radius
     L
249. lambdaFLambdaToJansky -- Inverse of janskyToLambdaFLambda (pass an array to get an array)
250. LbolFromLH2O -- Computes bolometric luminosity from water maser luminosity using Urquhart et al. 2001 Eq 9
251. loOffsetSuppression -- Computes suppression in dB according to Peter Napier's 2007 memo Appendix Eq 5
252. lsrkRangeForSpw -- Computes the LSRK frequencies of the first and last channel of the same spw in a list of measurement sets
     M
253. magjy -- Converts between magnitudes and Janskys for optical through mid-infrared wavelengths
254. makeFlagTimeRanges -- Builds an array of period timerange strings suitable for use in flagdata on simulated measurement sets
255. makemaskForNewLine -- Copies the clean mask from one line cube to another
256. makeMaskFromEstimatesFiles -- Builds an aggregate 2D mask from a list of imfit estimates files using circular apertures
257. makemaskImage -- Builds a mask image from an existing image and a mask lattice expression
258. makeNoiseImage -- Takes an image as a template and creates a noise image over the same area
259. makeNoiseSpectrum -- Makes an array of random numbers of a specified std and mean
260. makePolygonAnnulusRegionMask -- Builds an image of an annulus at a specified location with specified inner and outer radii
261. makeRobust1cubes -- Builds a script to run tclean to recreate pipeline image cubes with a different robust value
262. masercloud -- Makes a 3D plot of a sequence of maser spot files
263. maserLuminosity -- Computes luminosity for a spectral line
264. maserUpperLimit -- Computes lower limit to the maser increase factor when only upper limits are available from one epoch
265. maskChannel -- Mask a channel or range of channels in a CASA image cube
266. matchImfitEstimates -- Copies imfit estimates files for a prior cube that match in velocity to a new cube
267. meanEpoch -- Uses au.yearFraction to compute mean epoch of a list of dates
268. meanPosition -- Takes two sexagesimal directions and computes the mean of both axes to produce a new direction
269. measuredProperMotion -- Takes a measured shift in RA seconds and Dec arcseconds between 2 epochs, and computes proper motion and extrapolates for a third epoch
270. memo407 -- Reimplementation of the analysis of ALMA Memo 417 in numpy/scipy (for WSU SRR https://jira.alma.cl/browse/RID-2270)
271. mergebib -- Takes a .tex and .bbl file and puts the latter into the former, for submission to the ApJL word count tool
272. minimumMassSolarNebula -- computes mass in Msun for specified surface density, inner and outer radii using a 1/r^2 density profile
273. minimumSpanningTree -- Computes the minimum spanning tree of a graph
274. modifySpectrumInCube -- Stuffs a new spectrum of values into a spatial pixel of a CASA image cube
275. mom0mom8scaleFactor -- Compute factor by which to scale a mom0 image prior to subtracting from a mom8 image
276. montageUVspectraWithFindcont -- Compiles pipeline calibrated uv spectra alongside corresponding findContinuum spectra
277. monteCarloAddition -- Computes the joint uncertainty of a sum of measurements with individual uncertainties
278. monteCarloRatio -- Computes the uncertainty of a measurement scaled by an uncertain scale factor
     N
279. nanmean -- Returns scipy.stats.nanmean if numpy is earlier than 1.81, otherwise returns np.nanmean
280. nanmedian -- Returns scipy.stats.nanmedian if numpy is earlier than 1.81, otherwise returns np.nanmedian
281. nearestSourceInFitsTable -- Finds the nearest source in a FITS table to a specified direction
282. nextPowerOfTwo -- Computes the next power of 2 greater than or equal to the specified integer
283. noiseFigure -- Compute noise figure from noise temperature
284. ALMA.NoiseTemperatureFromNoiseFigure -- Compute noise temperature from noise figure
285. nonScanTimeRanges -- Returns a list of date/time ranges outside of the scans of a specified intent
286. northalign -- Uses the montage python wrapper to align a FITS image to north up
     O
287. offsetScanNumbers -- Adds a constant to the SCAN_NUMBER column of a measurement set
288. olnon -- Computes free-free spectral energy distribution from the models of Olnon 1975
289. oneEvent -- For a given population size, compute the sigma that gives just one event
290. optimalLevelSpacing -- Returns optimal level spacing from Table 1 of Thompson, Emerson and Schwab (2007)
291. optimalVoltageBinThresholds -- Determines the voltage bin thresholds for the spacing returned by tt.optimalLevelSpacing()
292. outburstEnergy -- Computes Joules in a protostellar outburst from luminosity and years
293. outermosaic -- Computes the border points of a mosaic pointing pattern
     P
294. phaseScreenCorrupt -- Corrupts a measurement set using the sm.settrop method.
295. photonStep -- Compute photon step for a specified frequency
296. pipelineBandpassTimeSolint -- Searches CASA log for longest time solint on bandpass calibartor
297. pipelineBeamRadius -- Emulates the calculation in imageparams_base.py
298. pipelineMeanVisibility -- Extracted code from gcorfluxscale.py
299. pipelineNantennas -- Returns number of antennas in first EB of a pipeline run
300. pipelinePhasecalSolint -- Checks for solint specified gaincal as a value in 's'econds, rather than 'int' or 'inf'
301. pipelinePlotmsMPIFraction -- Searches a pipeline casa log file, counts number of lines with "Executing plotms" and counts again for lines also containing "MPI" earlier on the line
302. pipelinePlottingTimes -- Computes time spent in making sky plots in hif_makeimages
303. pipelineSpwphaseupSpwmap -- finds the spwmap used by the pipeline in spwhpaseup
304. pipelineSpwBandwidths -- finds the bandwidths of the science spws of a pipeline run's MOUS
305. pipelineSpwInfo -- Reports a dictionary of science spws for a pipelien run with values of nChannels and bandwidth
306. pipelineSpwNChannels -- Reports number of channels per science spw in a pipeline run
307. pipe337beforeAfter -- Makes before/after plots for the hifa_targetflag flags
308. planckIntensity -- Computes the intensity of the Planck function
309. plotAplpyLines -- Plots a list of line segments from an ASCII file onto an aplpy figure
310. plotAplpyPositionAngle -- Plots a line along a position angle on an aplpy FitsFigure
311. plotATAC -- Plots frequency slices across the sidebands
312. plotATACB2B -- Calls plotATAC twice and stacks the plots into one png
313. plotATACBand2 -- Plots frequency slices across the sidebands of Band 2
314. plotATACBand8 -- Plots frequency slices across the sidebands of Band 8
315. plotCalibratorImagePeaks -- Plots an SED of the image peaks of the per-spw calibrator continuum images
316. plotCheckDurationOfBandpassScans -- Plots the dictionary returned by checkDurationOfBandpassScans
317. plotCompareFluxcsvs -- Plots age of spectral index vs. separationWindow, from several runs of compareFluxcsvs
318. plotCompareL80 -- Plots the results from compareL80list
319. plotFluxMaxAge -- Plots the SSR-generated file used by the OT in ICT-13764
320. plotHartRAO -- Plots maser spectra ascii files from HartRAO
321. plotHartRAODifference -- Plots the difference between two maser spectra ascii files from HartRAO
322. plotLinesOfCodeVsTime -- Plots the lines of code vs. cvs version number and vs. time
323. plotMaxHoldSpectrum -- Plots the maximum of a uv spectrum output by plotms text file tool
324. plotmsSWARM -- overlays the spws from many measurement sets into one plotms spectrum
325. plotNoiseCorrectionFactor -- plots the noise correction factor applied by the pipeline as defined in Todd's 13/Jul/2016 comment in CAS-8534 for the Hann window used by the ALMA baseline correlator (used for Fig 15 in the ALMA pipeline heuristics paper in PASP 2023)
326. plotRegionSpectrum -- computes and plots the spectrum from the unmasked pixels in a CASA region file
327. plotRobustGrid -- Plots the results file from buildRobustWeightingGrid
328. plotSMAEngineeringData -- plots data files downloaded from http://sma1.sma.hawaii.edu/internal/plot/customplots.html
329. plotSpwsVsTime -- Plots the science spws that appear in scans vs. time (or scan ID)
330. plotTimePipelineImaging -- Makes histograms from a dictionary created by checkTimePipelineImaging
331. plotTLEazel -- plots a satellite azimuth, elevation file produce by SxP4Test
332. polarizationUncertainty -- computes polarization percentage and its uncertainty from I, Q, U flux densities and image rms
333. properMotion -- computes proper motion in mas/year and beams/year for a specified distance, velocity and antenna configuration
334. propertiesForIonizingPhotonRateDiazMiller -- determine interpolated ZAMS stellar properties for the specified value of Lyman continuum photon rate
335. propertiesForSpectralTypeHanson -- determine interpolated ZAMS stellar properties for the specified spectral type
336. pruneMask -- Calls Tak's prune algorithm used by tclean autoboxing
     Q
337. quantizationCorrection -- Formulas 8.67 and 8.68 of TMS using optimal values of level separation (epsilon) from Thompson, Emerson and Schwab (2007)
338. quantizationEfficiencySlope -- Reads 5 files written by tt.memo407() for a given digitizer type and overlays them
339. quantumLimit -- Computes quantum limited Trx values for a given frequency
     R
340. radecListToOffsets -- Converts a list of sexagesimal RA/Dec values into relative coordinates in arcsec (relative to first position in the list)
341. randomGauss -- Return an array of n random numbers with the specified mean and standard deviation
342. readCommonVelocities -- Determines velocities shared by fits to two maser lines in G358
343. readPolygonRegion -- Reads a polygon shape from a CRTF file
344. readVisstatDict -- Reads a dictionary returned by the CASA task visstat that was stored in a plain text file.
345. regionSpectrum -- Computes the spectrum from a specified region of a CASA image
346. regionToEstimates -- Converts a CASA region file of positions to a imfit estimates file
347. relativeEfficiencySlope -- Reads 5 files written by tt.memo407() for a given digitizer type and overlays them
348. relaxationTime -- Computes relaxation time of a stellar cluster
349. removeNaNs -- remove (or replace) the NaNs from an array
350. removeLastLineOfFile -- removes the final line of an ASCII file, or list of files
351. removeLines -- removes all lines of an ASCII file that contain a specified string (used for culling AQUA/QA0 bugs in flag command txt files)
352. replaceMaskedPixels -- replaces masked pixels in a CASA image with a specified value
353. replaceSpacesInFilenames -- replaces spaces with blanks or another character in a filename (or list thereof)
354. replaceStringInFiles -- replaces a string with another string in a list of files
355. rmsJitterSeconds -- Converts points measured on an Allan variance curve of dBc/Hz vs. Hz into rms jitter in seconds
356. robitailleLuminosity -- integrates the lambda*F_lambda SED of a Robitaille model to compute apparment luminosity
357. robitailleStefanBoltzmann -- reads a text file of best fitting Robitaille models and computes luminosity of protostar from Teff and radius
358. rotationPhase -- determines the rotational phase of an observation relative to a zero point in the past
     S
359. roundMeasurementToAsymmetricString -- converts a value and uncertainty to a latex string with different + and - error bars
360. roundMeasurementToAsymmetricScientificString -- converts a value and uncertainty to a latex string in scientific notation with different + and - error bars
361. roundMeasurementToScientificString -- converts a value and uncertainty to a latex string in scientific notation
362. roundMeasurementToString -- converts a value and uncertainty to a string
363. scaleFluxcsv -- Scales the flux densities in an ALMA pipeline's flux.csv file
364. scaleImage -- Scales the intensity in one or more rectangular boxes in a CASA image by a scale factor
365. scaleImageSize -- Takes a string like '100x60' and scales each number by a specified factor
366. scanTimeRanges -- Returns a list of date/time ranges for all the scans of a specified intent
367. shadowedArea -- Computes percentage of antenna area shadowed for a given linear overlap
368. shiftDecString -- Takes a sexagesimal format Dec Value and shifts it by a specified value of arcseconds
369. shiftPolygonRegion -- Reads a polygon region from a CRTF file, shifts it a specified amount and writes a new CRTF file
370. shiftRAString -- Takes a sexagesimal format RA value and shifts it by a specified value of arcseconds
371. shortenCasalog -- Removes all messages from CASA tasks (helpful when debugging non-tasks)
372. show_circles_intersecting -- Implements aplpy's show_circles but prevents drawing portions that overlap other circles.
373. sigmaEvent -- compute the probability of an N-sigma event
374. sisLOPowerRequirement -- Compute LO power required for a specified frequency, junction resistance and coupling factor
375. sisOptimalImpedance -- Compute optimal impedance for an SIS mixer tuning circuit
376. specfitPlot -- Plots the fit result from the CASA task specfit
377. spectralTypeFloatToStringTo -- converts 0.95 to 'O9.5' for use after interpolating tables
378. spectralTypeSternberg -- returns spectral type and luminosity for Q value for class V stars
379. spectralTypeStringToFloat -- converts 'O9.5' to 0.95 for use in interpolating tables
380. spectralTypeToTemperature -- uses Pecaut & Mamajek 2013 to convert spectral type to surface temperature
381. spectraOverlay -- Reads and plots a spectral profile ASCII file created by the CASA viewer
382. splitSedResults -- Split an sed_results file into N files to prepare it for Robitaille's fitter
383. squintScatterPlot -- Compares the on telescope measurements with FEIC measurements
384. stefanBoltzmannLuminosity -- convert radius, distance and temperature to luminosity
385. stefanBoltzmannRadius -- convert luminosity and temperature to radius
386. stefanBoltzmannTemperature -- convert luminosity and radius to temperature
387. stringToURL -- convert a text string to an encoded version suitable for use in a URL
     T
388. tauFromBrightness -- Inverts the equation Tb = T*(1-exp(-tau))
389. temperatureToSpectralType -- interpolates Table 5 of Pecaut & Mamajek 2013
390. testDigitizeSignal -- Runs tt.digitizeSignal() and plots the results overlaid with the input signal.
391. timegaincalInterval -- Reads the bandpass/flux phase-only solint from the timegaincal weblog table
392. tms832 -- Equation 8.32 of TMS
393. tms835 -- Equation 8.35 of TMS
394. ALMA.TmsTable71ampSlope -- Equation for SNR degradation due to amplitude slope across a single correlator channel from Table 7.1 row 1 of TMS
395. toneStrength -- Computes strength of line in K and Jy that contributes a specified percentage of the subband total power
396. topoFreqToChannel -- Converts a list of topo frequencies to topo channels in a measurement set
397. topoFreqRangeListToChannel -- Converts a semicolon-delimit list of frequency ranges to topo channel ranges
398. toutZAMS -- Computes radius, luminosity and temperature for a ZAMS star as a function of mass and metallicity
399. truncatedJDToDatestring -- converts truncated JD to date string
400. tskyGridPlot -- makes a grid of plots of Tsky vs. frequency from a list of measurement sets and maxAltitudes
     V
401. uncertaintyOfSummedValues -- computes uncertainty of a sum of measurements
     V
402. vacuumWindowLoss -- computes loss through a material of specified thickness, index and tan delta
403. velocityChannelWidth -- Returns the width of cube channels in velocity units
404. version -- returns the CVS version number of toddTools.py
405. visibleSky -- compute the fraction of the sky ever visible from a specified latitude and horizon limit
406. vislistFromFluxcsv -- Returns list of measurement sets contained a flux.csv file
     W
407. widthOfMaskArcsec -- Finds the width of the smallest central square that circumscribes a mask
408. wsuspw -- For a specified spw width (in units of FS) and desired spectral resolution, returns a dictionary keyed by nchan with values being a sub-dictionary of information for the parent setup and each CAF multiple that resultin an integer number of output channels of equal sensitivity
409. wsuspwMatrix Produces a terminal display (space-delimited for readability) and a text file (comma-delimited for import into spreadsheets) of possible spw combinations for each element in a list of number of adjacent frequency slices.
     Z
410. zams -- Computes luminosity and radius for a given stellar mass using Hosokawa's fits to Schaller et al. 1992
411. zamsMassFromLuminosity -- Computes empirical relation of Demircan and Kahraman 1991
412. zeeman -- fits Stokes I and V spectra for Zeeman effect and magnetic field

-- ToddHunter - 2014-08-13