Documentation of functions in toddTools.py

Return to directory of CASA extensions in analysisUtils.py

The toddTools package is an extension of simple python tasks for radio/millimeter/submillimeter astronomy and star formation studies mean to run inside the monolithic CASA environment. It can also be imported into plain python, but tasks that require CASA tasks or tools will not function in that environment. Some of the tasks are reliant upon functions in the analysisUtils package of ALMA. While toddTools is not (yet) publicly-available, subsets of the code will be made available upon reasonable request to the author.

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

-- ToddHunter - 2014-08-13