Begin removal of analysisUtils

CHANGELOG.md

@@ -40,6 +40,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Use spectral-cube common beam calculations for common beams (#385).
 - Mosaic weights are now generated after convolution and regridding, and will undo any primary beam corrections (#396).
 - Don't skip making large mosaics (but keep the log messages to inform users this is happening) (#405).
+- Begin removal of analysisUtils (#402).
 
 ### Fixed
 

phangsPipeline/casaCubeRoutines.py

@@ -7,7 +7,6 @@
 import logging
 import os
 
-import analysisUtils as au
 import numpy as np
 import scipy.ndimage as nd
 from astropy.io import fits
@@ -45,7 +44,7 @@ def check_getchunk_putchunk_memory_issue(
 
     Args:
         infile: input image file.
-        myia: optional, if not given then we will run `myia = au.createCasaTool(casaStuff.iatool)` then `myia.open(infile)`.
+        myia: optional, if not given then we will run `myia = casaStuff.iatool()` then `myia.open(infile)`.
         return_data: if True then we will return the data if `getchunk()` runs properly withut a memory issue.
         return_mask: if True then we will return the mask if `getchunk(getmask=True)` runs properly withut a memory issue.
         return_shape: if True then we will return the shape of the cube data.
@@ -64,7 +63,7 @@ def check_getchunk_putchunk_memory_issue(
     cube_mask = None
     has_opened_file = False
     if myia is None:
-        myia = au.createCasaTool(casaStuff.iatool)
+        myia = casaStuff.iatool()
         myia.open(infile)
         has_opened_file = True
     if not myia.isopen():
@@ -177,14 +176,14 @@ def get_mask(infile, huge_cube_workaround=True):
     #    os.system('rm -rf ' + infile + '.temp.fits')
     #
     #else:
-    #    myia = au.createCasaTool(casaStuff.iatool)
+    #    myia = casaStuff.iatool()
     #    myia.open(infile+'.temp_deg')
     #    mask = myia.getchunk(getmask=True)
     #    myia.close()
     #
     #os.system('rm -rf ' + infile + '.temp_deg')
 
-    myia = au.createCasaTool(casaStuff.iatool)
+    myia = casaStuff.iatool()
 
     myia.open(infile)
 
@@ -237,7 +236,7 @@ def copy_mask(infile, outfile, huge_cube_workaround=True):
 
     # use putregion to update pixel mask
 
-    myia = au.createCasaTool(casaStuff.iatool)
+    myia = casaStuff.iatool()
 
     myia.open(outfile)
 
@@ -259,7 +258,7 @@ def copy_mask(infile, outfile, huge_cube_workaround=True):
     else: # getchunk was unsuccessful, has memory issue
         # putregion channel by channel
         logger.debug('putregion channel by channel for known memory issue')
-        myrg = au.createCasaTool(casaStuff.rgtool)
+        myrg = casaStuff.rgtool()
         nx = out_shape[0]
         ny = out_shape[1]
         #logger.debug('copy_mask mask.shape {}'.format(mask.shape))
@@ -324,13 +323,13 @@ def multiply_cube_by_value(infile, value, brightness_unit, huge_cube_workaround=
     #                         overwrite=True)
     #    os.system('rm -rf ' + infile + '.fits')
     #else:
-    #    myia = au.createCasaTool(casaStuff.iatool)
+    #    myia = casaStuff.iatool()
     #    myia.open(infile)
     #    vals = myia.getchunk()
     #    vals *= value
     #    myia.putchunk(vals)
 
-    myia = au.createCasaTool(casaStuff.iatool)
+    myia = casaStuff.iatool()
 
     myia.open(infile)
 
@@ -627,7 +626,7 @@ def trim_rind(
         target_file = infile
 
     # Figure out the extent of the image inside the cube
-    myia = au.createCasaTool(casaStuff.iatool)
+    myia = casaStuff.iatool()
     myia.open(target_file)
     mask = myia.getchunk(getmask=True)
     elt = nd.generate_binary_structure(2,1)

phangsPipeline/casaFeatherRoutines.py

@@ -6,7 +6,6 @@
 import logging
 import os
 
-import analysisUtils as au
 import numpy as np
 
 from . import casaCubeRoutines as ccr
@@ -115,12 +114,12 @@ def prep_sd_for_feather(
             overwrite=overwrite)
 
     # Get out and match axis orders from interferometric images
-    myia = au.createCasaTool(casaStuff.iatool)
+    myia = casaStuff.iatool()
     myia.open(interf_file)
     interf_cs = myia.coordsys()
     myia.close()
 
-    myia = au.createCasaTool(casaStuff.iatool)
+    myia = casaStuff.iatool()
     myia.open(current_outfile)
     sd_cs = myia.coordsys()
     myia.close()
@@ -235,7 +234,7 @@ def feather_two_cubes(
         os.system('cp -rf '+interf_file+' '+current_interf_file)
         os.system('cp -rf '+sd_file+' '+current_sd_file)
 
-        myia = au.createCasaTool(casaStuff.iatool)
+        myia = casaStuff.iatool()
 
         # As noted in [https://casa.nrao.edu/docs/casaref/image.putchunk.html], 
         # "If all the pixels didn't easily fit in memory, you would iterate through 
@@ -390,7 +389,7 @@ def feather_two_cubes(
 
     # Finally, if we don't have a 4th (Stokes I) axis, add this
     # here to avoid feather crashing
-    myia = au.createCasaTool(casaStuff.iatool)
+    myia = casaStuff.iatool()
 
     myia.open(current_interf_file)
     interf_shape = myia.shape()

phangsPipeline/casaImagingRoutines.py

@@ -7,11 +7,11 @@
 import logging
 import os
 
-import analysisUtils as au
 import numpy as np
 
 from . import casaMaskingRoutines as cmr
 from . import casaStuff
+from .casaVisRoutines import get_spw_info, pick_cell_and_im_size
 from .clean_call import CleanCall
 
 logger = logging.getLogger(__name__)
@@ -50,65 +50,21 @@ def estimate_cell_and_imsize(
     else:
         pblevel = clean_call.get_param('pblimit')
 
-    # These are the CASA-preferred sizes for fast FFTs
-
-    valid_sizes = []
-    for ii in range(10):
-        for kk in range(3):
-            for jj in range(3):
-                valid_sizes.append(2 ** (ii + 1) * 5 ** jj * 3 ** kk)
-    valid_sizes = sorted(valid_sizes)
-    valid_sizes = np.array(valid_sizes)
-
-    # Cell size implied by baseline distribution from analysis
-    # utilities.
-
-    au_cellsize, au_imsize, _ = au.pickCellSize(infile,
-                                                imsize=True,
-                                                npix=oversamp,
-                                                intent='',
-                                                pblevel=pblevel,
-                                                )
-    xextent = au_cellsize * au_imsize[0] * 1.2
-    yextent = au_cellsize * au_imsize[1] * 1.2
-
-    # Make the cell size a nice round number
-
-    if au_cellsize < 0.01:
-        cell_size = au_cellsize
-    elif 0.01 <= au_cellsize < 0.05:
-        cell_size = np.floor(au_cellsize / 0.005) * 0.005
-    elif 0.05 <= au_cellsize < 0.1:
-        cell_size = np.floor(au_cellsize / 0.01) * 0.01
-    elif 0.1 <= au_cellsize < 0.5:
-        cell_size = np.floor(au_cellsize / 0.05) * 0.05
-    elif 0.5 <= au_cellsize < 1.0:
-        cell_size = np.floor(au_cellsize / 0.1) * 0.1
-    elif 1.0 <= au_cellsize < 2.0:
-        cell_size = np.floor(au_cellsize / 0.25) * 0.25
-    elif 2.0 <= au_cellsize < 5.0:
-        cell_size = np.floor(au_cellsize / 0.5) * 0.5
-    else:
-        cell_size = np.floor(au_cellsize / 1.0) * 0.5
-
-    # Now make the image size a good number for the FFT
-
-    need_cells_x = xextent / cell_size
-    need_cells_y = yextent / cell_size
-
-    cells_x = np.min(valid_sizes[valid_sizes > need_cells_x])
-    cells_y = np.min(valid_sizes[valid_sizes > need_cells_y])
+    # Cell size implied by baseline distribution
+    cell_size, image_size = pick_cell_and_im_size(
+        infile,
+        npix=oversamp,
+        pblevel=pblevel,
+    )
 
     # If requested, force the mosaic to be square. This avoids
     # pathologies in CASA versions 5.1 and 5.3.
-
     if force_square:
-        if cells_y < cells_x:
-            cells_y = cells_x
-        if cells_x < cells_y:
-            cells_x = cells_y
+        if image_size[0] < image_size[1]:
+            image_size[1] = image_size[0]
+        if image_size[0] > image_size[1]:
+            image_size[0] = image_size[1]
 
-    image_size = [int(cells_x), int(cells_y)]
     cell_size_string = str(cell_size) + 'arcsec'
 
     return cell_size_string, image_size
@@ -786,18 +742,17 @@ def clean_loop(
     working_call.set_param('calcpsf', False)
 
     # Note the number of channels, which is used in setting the number
-    # of iterations that we give to an individual clean call.
-
-    vm = au.ValueMapping(working_call.get_param('vis'))
-
-    # If we have a number of channels defined, then use that
+    # of iterations that we give to an individual clean call. If we
+    # have a number of channels defined, then use that
     nchan = working_call.get_param('nchan')
 
     # Otherwise, pull the total number of channels from the spwInfo
     if nchan is None:
         nchan = -1
     if nchan <= 0:
-        nchan = vm.spwInfo[0]['numChannels']
+        vis = working_call.get_param('vis')
+        spw_info = get_spw_info(vis)
+        nchan = spw_info[0]['numChannels']
 
     # Create a text record of progress through successive clean calls.
 
@@ -1016,7 +971,7 @@ def clean_loop(
             pb_image = (_imagename + '.pb') if _imagename else None
             if pb_image and os.path.isdir(pb_image):
                 try:
-                    myia = au.createCasaTool(casaStuff.iatool)
+                    myia = casaStuff.iatool()
                     myia.open(pb_image)
                     pb_data = myia.getchunk()
                     myia.close()
@@ -1115,7 +1070,7 @@ def calc_residual_statistics(
         logger.error('Error! The input file "' + mask_name + '" was not found!')
         return
 
-    myia = au.createCasaTool(casaStuff.iatool)
+    myia = casaStuff.iatool()
 
     myia.open(mask_name)
     mask = myia.getchunk()