casa / casa5 / ea2e9c50578

Commits

David Mehringer authored ea2e9c50578 26 Jun 2013

        New Development: No             JIRA Issue: CAS-5261          Ready for Test: Yes      Interface Changes: No What Interface Changed: Please list interface changes          Test Programs: List test programs   Put in Release Notes: Yes/No              Module(s): Module Names change impacts.            Description: Added exception handling, dimensionality checking, and documentation

gcwrap/python/scripts/task_boxit.py

Modified

-1
+from taskinit import *
-2
+import numpy
-3
+import sys
-4
+import re
-5
-6
+# Writes out regions above threshold to regionfile+'.box'
-7
-8
+def boxit(imagename, regionfile, threshold, maskname, chanrange, polrange, minsize, diag, boxstretch, overwrite):
-9
-10
+    casalog.origin('boxit')
--
--
+    if not(regionfile):
--
+        regionfile = imagename + '.box'
--
+    if not regionfile.endswith('.box'):
--
+        regionfile = regionfile + '.box'
--
--
+    if not(overwrite):
--
+        if(os.path.exists(regionfile)):
--
+            casalog.post('file "' + regionfile + '" already exists.', 'WARN')
--
+            return
--
+        if(maskname and os.path.exists(maskname)):
--
+            casalog.post('output mask "' + maskname + '" already exists.', 'WARN')
-+
+    myia = iatool()
-+
+    try:
-+
+        if not(regionfile):
-+
+            regionfile = imagename + '.box'
-+
+        if not regionfile.endswith('.box'):
-+
+            regionfile = regionfile + '.box'
-+
-+
+        if not(overwrite):
-+
+            if(os.path.exists(regionfile)):
-+
+                casalog.post('file "' + regionfile + '" already exists.', 'WARN')
-+
+                return
-+
+            if(maskname and os.path.exists(maskname)):
-+
+                casalog.post('output mask "' + maskname + '" already exists.', 'WARN')
-+
+                return
-+
-+
+        # If no units, assume mJy for consistency with auto/clean tasks.
-+
+        # But convert to Jy, because that's what units the images are in.
-+
+        threshold = qa.getvalue(qa.convert(qa.quantity(threshold,'mJy'),'Jy'))[0]
-+
+        casalog.post("Setting threshold to " + str(threshold) + "Jy", "INFO")
-+
+        newIsland = numpy.zeros(1, dtype=[('box','4i4'),('npix','i4')])
-+
+        # Find all pixels above the threshold
-+
+        myia.open(imagename)
-+
+        if len(myia.shape()) != 4:
-+
+            raise Exception("Only 4D images with direction, spectral, and stokes coordinates are supported")
-+
+        # CAS-2059 escape characters in image name that will confuse the lattice expression processor
-+
+        escaped_imagename = imagename
-+
+        for escapeme in ['-', '+', '*', '/' ]:
-+
+            escaped_imagename = re.sub("[" + escapeme + "]", "\\" + escapeme, escaped_imagename)
-+
+        mask = escaped_imagename+'>'+str(threshold)
-+
+        fullmask = myia.getregion(mask=mask, getmask=True)
-+
+        if not(fullmask.max()):
-+
+            casalog.post('Maximum flux in image is below threshold.', 'WARN')
-43
+            return
--
--
+    # If no units, assume mJy for consistency with auto/clean tasks.
--
+    # But convert to Jy, because that's what units the images are in.
--
+    threshold = qa.getvalue(qa.convert(qa.quantity(threshold,'mJy'),'Jy'))[0]
--
+    casalog.post("Setting threshold to " + str(threshold) + "Jy", "INFO")
--
--
+    newIsland = numpy.zeros(1, dtype=[('box','4i4'),('npix','i4')])
--
+    # Find all pixels above the threshold
--
+    ia.open(imagename)
--
+    # CAS-2059 escape characters in image name that will confuse the lattice expression processor
--
+    escaped_imagename = imagename
--
+    for escapeme in ['-', '+', '*', '/' ]:
--
+        escaped_imagename = re.sub("[" + escapeme + "]", "\\" + escapeme, escaped_imagename)
--
+    mask = escaped_imagename+'>'+str(threshold)
--
+    fullmask = ia.getregion(mask=mask, getmask=True)
--
+    if not(fullmask.max()):
--
+        casalog.post('Maximum flux in image is below threshold.', 'WARN')
--
+        return
--
+    writemask = bool(maskname)
--
+    csys = ia.coordsys()
--
--
+    shape = fullmask.shape
--
--
+    nx = int(shape[0])
--
+    ny = int(shape[1])
--
+    n2 = n3 = 1
--
+    if len(shape)==3:
--
+        n2 = int(shape[2])
--
+    if len(shape)==4:
--
+        n2 = int(shape[2])
--
+        n3 = int(shape[3])
--
+    #print 'nx:', nx, 'ny:', ny, 'n2:', n2, 'n3:', n3
--
--
+    #casa generated images always 4d and in order of [ra, dec, stokes, freq]
--
+    #other images can be in the order of [ra, dec, freq, stokes]
--
+    nms = csys.names()
--
+    #axes=[]
--
+    #for i in xrange(len(nms)):
--
+    #   if nms[i]=='Right Ascension':
--
+    #      axes[0]=i
--
+    #   if nms[i]=='Declination':
--
+    #      axes[1]=i
--
+    #   if nms[i]=='Stokes'
--
+    #      axes[2]=i
--
+    #   if nms[i]=='Frequency':
--
+    #      axes[3]=i
--
--
+    chmax=n3
--
+    pomax=n2
--
+    chmin=0
--
+    pomin=0
--
+    if len(nms)==4 and nms[3]=='Stokes':
--
+       chmax=n2
--
+       pomax=n3
--
--
+    if chanrange:
--
+       try:
--
+          if str.count(chanrange, '~') == 1:
--
+             ch1=int(str.split(chanrange, '~')[0])
--
+             ch2=int(str.split(chanrange, '~')[1])
--
+          else:
--
+             ch1=int(chanrange)
--
+             ch2=ch1
--
+          if ch1 > ch2 or ch1 < 0 or ch2 > chmax:
--
+             casalog('invalid channel range', "SEVERE")
--
+             return
--
+          if ch1>chmin:
--
+             chmin = ch1
--
+          if ch2<chmax:
--
+             chmax = ch2
--
+       except:
--
+          casalog('bad format for chanrange', "SEVERE")
--
+          return
--
+    #print 'chmin', chmin, 'chmax', chmax
--
--
+    if polrange:
--
+       try:
--
+          if str.count(polrange, '~') == 1:
--
+             po1=int(str.split(polrange, '~')[0])
--
+             po2=int(str.split(polrange, '~')[1])
--
+          else:
--
+             po1=int(polrange)
--
+             po2=po1
--
+          if po1 > po2 or po1 < 0 or po2 > pomax:
--
+             casalog( 'invalid stokes range', "SEVERE")
--
+             return
--
+          if po1>pomin:
--
+             pomin = po1
--
+          if po2<pomax:
--
+             pomax = po2
--
+       except:
--
+          casalog( 'bad format for polrange', "SEVERE")
--
+          return
--
+    #print 'pomin', pomin, 'pomax', pomax
--
--
+    n1=pomin
--
+    n2=pomax
--
+    n3=chmax
--
+    n4=chmin
--
+    if len(nms)==4 and nms[3]=='Stokes':
--
+       n1=chmin
--
+       n2=chmax
--
+       n3=pomax
--
+       n4=pomin
--
+    #print 'n1:', n1, 'n2:', n2, 'n4:', n4, 'n3:', n3
-+
+        writemask = bool(maskname)
-+
+        csys = myia.coordsys()
-46
--
+    f = open(regionfile, 'w')
--
+    totregions = 0
--
+    outputmask = []
--
+    if writemask:
--
+        outputmask = ia.getchunk()
--
+        outputmask.fill(False)
--
--
+    for i3 in xrange(n4, n3):
--
+        for i2 in xrange(n1, n2):
--
+            regions = {}
--
+            boxRecord = {}
--
+            if len(shape)==2:
--
+                mask = fullmask
--
+            if len(shape)==4:
--
+                mask = fullmask[:,:,i2,i3].reshape(nx, ny)
--
+            islands = []
--
+            pos = numpy.unravel_index(mask.argmax(), mask.shape)
--
+            #print pos
--
+            while(mask[pos]):
--
+                # found pixel in new island
--
+                island = {}
--
+                island['box'] = [pos[0], pos[1], pos[0], pos[1]]
--
+                island['npix'] = 1
--
+                find_nearby_island_pixels(island, mask, pos, shape[0], shape[1], diag)
--
+                islands.append(island)
-+
+        shape = fullmask.shape
-+
+        nx = int(shape[0])
-+
+        ny = int(shape[1])
-+
+        n2 = n3 = 1
-+
+        if len(shape)==3:
-+
+            n2 = int(shape[2])
-+
+        if len(shape)==4:
-+
+            n2 = int(shape[2])
-+
+            n3 = int(shape[3])
-+
-+
+        #casa generated images always 4d and in order of [ra, dec, stokes, freq]
-+
+        #other images can be in the order of [ra, dec, freq, stokes]
-+
+        nms = csys.names()
-+
-+
+        chmax=n3
-+
+        pomax=n2
-+
+        chmin=0
-+
+        pomin=0
-+
+        if len(nms)==4 and nms[3]=='Stokes':
-+
+           chmax=n2
-+
+           pomax=n3
-+
+        if chanrange:
-+
+           try:
-+
+              if str.count(chanrange, '~') == 1:
-+
+                 ch1=int(str.split(chanrange, '~')[0])
-+
+                 ch2=int(str.split(chanrange, '~')[1])
-+
+              else:
-+
+                 ch1=int(chanrange)
-+
+                 ch2=ch1
-+
+              if ch1 > ch2 or ch1 < 0 or ch2 > chmax:
-+
+                 casalog('invalid channel range', "SEVERE")
-+
+                 return
-+
+              if ch1>chmin:
-+
+                 chmin = ch1
-+
+              if ch2<chmax:
-+
+                 chmax = ch2
-+
+           except:
-+
+              casalog('bad format for chanrange', "SEVERE")
-+
+              return
-+
-+
+        if polrange:
-+
+           try:
-+
+              if str.count(polrange, '~') == 1:
-+
+                 po1=int(str.split(polrange, '~')[0])
-+
+                 po2=int(str.split(polrange, '~')[1])
-+
+              else:
-+
+                 po1=int(polrange)
-+
+                 po2=po1
-+
+              if po1 > po2 or po1 < 0 or po2 > pomax:
-+
+                 casalog( 'invalid stokes range', "SEVERE")
-+
+                 return
-+
+              if po1>pomin:
-+
+                 pomin = po1
-+
+              if po2<pomax:
-+
+                 pomax = po2
-+
+           except:
-+
+              raise Exception('bad format for polrange')
-+
+        n1=pomin
-+
+        n2=pomax
-+
+        n3=chmax
-+
+        n4=chmin
-+
+        if len(nms)==4 and nms[3]=='Stokes':
-+
+           n1=chmin
-+
+           n2=chmax
-+
+           n3=pomax
-+
+           n4=pomin
-+
-+
+        f = open(regionfile, 'w')
-+
+        totregions = 0
-+
+        outputmask = []
-+
+        if writemask:
-+
+            outputmask = myia.getchunk()
-+
+            outputmask.fill(False)
-+
+        for i3 in xrange(n4, n3):
-+
+            for i2 in xrange(n1, n2):
-+
+                regions = {}
-+
+                boxRecord = {}
-+
+                if len(shape)==2:
-+
+                    mask = fullmask
-+
+                if len(shape)==4:
-+
+                    mask = fullmask[:,:,i2,i3].reshape(nx, ny)
-+
+                islands = []
-129
+                pos = numpy.unravel_index(mask.argmax(), mask.shape)
--
+            for record in islands:
--
+                box = record['box']
--
+                # check size of box
--
+                if record['npix'] < minsize:
--
+                    continue
--
+                totregions += 1
--
+                # need pixel corners, not pixel centers
--
+                box[0] -= boxstretch
--
+                box[1] -= boxstretch
--
+                box[2] += boxstretch
--
+                box[3] += boxstretch
--
+                # in case we used boxstretch < 0 and a one-pixel sized box:
--
+                if box[0] > box[2]:
--
+                    box[0] += boxstretch
--
+                    box[2] -= boxstretch
--
+                if box[1] > box[3]:
--
+                    box[1] += boxstretch
--
+                    box[3] -= boxstretch
--
+                if writemask:
--
+                    # avoid pixels in boxes that have been stretched beyond the image limits
--
+                    for ii in range(max(0, box[0]), min(box[2], outputmask.shape[0] - 1)):
--
+                        for jj in range(max(0, box[1]), min(box[3], outputmask.shape[1] - 1)):
--
+                            outputmask[ii][jj][i2][i3] = True
--
+                blccoord = [box[0]-0.5, box[1]-0.5, i2, i3]
--
+                trccoord = [box[2]+0.5, box[3]+0.5, i2, i3]
--
+                # note that the toworld() calls are likely very expensive for many boxes. But then
--
+                # again, the box-finding algorithm itself seems pretty inefficient, but resource
--
+                # constraints only permit a band aid fix at this time.
--
+                blc = ia.toworld(blccoord, 'm')['measure']
--
+                trc = ia.toworld(trccoord, 'm')['measure']
--
+                # RA/Dec reference frame
--
+                outstring = "worldbox " + blc['direction']['refer']
--
+                # RA blc/trc
--
+                outstring += " [" + quantity_to_string(blc["direction"]["m0"], "rad") + ", "
--
+                outstring += quantity_to_string(trc["direction"]["m0"], "rad") + "]"
--
+                # Dec blc/trc
--
+                outstring += " [" + quantity_to_string(blc["direction"]["m1"], "rad") + ", "
--
+                outstring += quantity_to_string(trc["direction"]["m1"], "rad") + "]"
--
+                # frequency blc/trc
--
+                freq = blc["spectral"]['frequency']['refer'] + " "
--
+                freq += quantity_to_string(blc["spectral"]["frequency"]["m0"], "Hz", False)
--
+                outstring += " ['" + freq + "', '" + freq + "']"
--
+                # Stokes blc/trc
--
+                outstring += " ['" + blc["stokes"] + "', '" + trc["stokes"] + "']"
--
+                # add the mask flag
--
+                outstring += " " + str(1)
--
+                f.write(outstring + "\n")
--
+    casalog.post("Wrote " + str(totregions) + " regions to file " + regionfile, 'INFO')
--
+    if writemask:
--
+        myia = iatool()
--
+        myia.fromimage(infile=imagename, outfile=maskname, overwrite=True)
--
+        myia.done()
--
+        myia.open(maskname)
--
+        myia.putchunk(outputmask)
--
+        myia.done()
--
+    f.close()
--
+    return True
-+
+                while(mask[pos]):
-+
+                    # found pixel in new island
-+
+                    island = {}
-+
+                    island['box'] = [pos[0], pos[1], pos[0], pos[1]]
-+
+                    island['npix'] = 1
-+
+                    find_nearby_island_pixels(island, mask, pos, shape[0], shape[1], diag)
-+
+                    islands.append(island)
-+
+                    pos = numpy.unravel_index(mask.argmax(), mask.shape)
-+
+                for record in islands:
-+
+                    box = record['box']
-+
+                    # check size of box
-+
+                    if record['npix'] < minsize:
-+
+                        continue
-+
+                    totregions += 1
-+
+                    # need pixel corners, not pixel centers
-+
+                    box[0] -= boxstretch
-+
+                    box[1] -= boxstretch
-+
+                    box[2] += boxstretch
-+
+                    box[3] += boxstretch
-+
+                    # in case we used boxstretch < 0 and a one-pixel sized box:
-+
+                    if box[0] > box[2]:
-+
+                        box[0] += boxstretch
-+
+                        box[2] -= boxstretch
-+
+                    if box[1] > box[3]:
-+
+                        box[1] += boxstretch
-+
+                        box[3] -= boxstretch
-+
+                    if writemask:
-+
+                        # avoid pixels in boxes that have been stretched beyond the image limits
-+
+                        for ii in range(max(0, box[0]), min(box[2], outputmask.shape[0] - 1)):
-+
+                            for jj in range(max(0, box[1]), min(box[3], outputmask.shape[1] - 1)):
-+
+                                outputmask[ii][jj][i2][i3] = True
-+
+                    blccoord = [box[0]-0.5, box[1]-0.5, i2, i3]
-+
+                    trccoord = [box[2]+0.5, box[3]+0.5, i2, i3]
-+
+                    # note that the toworld() calls are likely very expensive for many boxes. But then
-+
+                    # again, the box-finding algorithm itself seems pretty inefficient, but resource
-+
+                    # constraints only permit a band aid fix at this time.
-+
+                    blc = myia.toworld(blccoord, 'm')['measure']
-+
+                    trc = myia.toworld(trccoord, 'm')['measure']
-+
+                    # RA/Dec reference frame
-+
+                    outstring = "worldbox " + blc['direction']['refer']
-+
+                    # RA blc/trc
-+
+                    outstring += " [" + quantity_to_string(blc["direction"]["m0"], "rad") + ", "
-+
+                    outstring += quantity_to_string(trc["direction"]["m0"], "rad") + "]"
-+
+                    # Dec blc/trc
-+
+                    outstring += " [" + quantity_to_string(blc["direction"]["m1"], "rad") + ", "
-+
+                    outstring += quantity_to_string(trc["direction"]["m1"], "rad") + "]"
-+
+                    # frequency blc/trc
-+
+                    freq = blc["spectral"]['frequency']['refer'] + " "
-+
+                    freq += quantity_to_string(blc["spectral"]["frequency"]["m0"], "Hz", False)
-+
+                    outstring += " ['" + freq + "', '" + freq + "']"
-+
+                    # Stokes blc/trc
-+
+                    outstring += " ['" + blc["stokes"] + "', '" + trc["stokes"] + "']"
-+
+                    # add the mask flag
-+
+                    outstring += " " + str(1)
-+
+                    f.write(outstring + "\n")
-+
+        casalog.post("Wrote " + str(totregions) + " regions to file " + regionfile, 'INFO')
-+
+        if writemask:
-+
+            myia.fromimage(infile=imagename, outfile=maskname, overwrite=True)
-+
+            myia.done()
-+
+            myia.open(maskname)
-+
+            myia.putchunk(outputmask)
-+
+            myia.done()
-+
+        f.close()
-+
+        return True
-+
+    except Exception, instance:
-+
+        casalog.post( str( '*** Error *** ') + str(instance), 'SEVERE')
-+
+        raise
-+
+    finally:
-+
+        if myia:
-+
+            myia.done()
-200
-201
+def quantity_to_string(quantity, unit=None, quotes=True):
-202
+    if unit != None:
-203
+        quantity = qa.convert(quantity, unit)
-204
+    string = str(quantity['value']) + quantity['unit']
-205
+    if quotes:
-206
+        string = "'" + string + "'"
-207
+    return string
-208
-209
+def find_nearby_island_pixels(island, mask, pos, xmax, ymax, diag):

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