pymakeplots 0.2.4__py3-none-any.whl → 0.2.6__py3-none-any.whl

pymakeplots/pymakeplots.py

@@ -9,8 +9,9 @@ import matplotlib.pyplot as plt
 import matplotlib
 from pymakeplots.sauron_colormap import sauron
 from mpl_toolkits.axes_grid1 import make_axes_locatable
-from matplotlib.patches import Ellipse,Rectangle, Arrow
+from matplotlib.patches import Ellipse,Rectangle, Arrow, FancyArrowPatch
 from matplotlib import cm
+from matplotlib.text import Text
 from matplotlib.colors import ListedColormap, LinearSegmentedColormap
 from matplotlib.offsetbox import AnchoredText,AuxTransformBox, AnchoredOffsetbox
 from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar,AnchoredDirectionArrows
@@ -54,12 +55,16 @@ class pymakeplots:
         self.pbcorr_cube=None
         self.spectralcube=None
         self.mask=None
+        self.masksmoothing=0
+        self.maskdilating=0
         self.flat_cube_trim=None
         self.pbcorr_cube_trim=None
         self.mask_trim=None
+        self.pbcliplevel=None
         self.bmaj=None
         self.rotate=rotate
         self.smoothmask_spatial=1.5
+        self.smoothmask_velocity=4
         self.bmin=None
         self.bpa=None
         self.xcoord,self.ycoord,self.vcoord = None, None, None
@@ -96,6 +101,7 @@ class pymakeplots:
         self.suppress_subbeam_artifacts=False
         self.mom1_cmap=sauron
         self.mom2_cmap=sauron
+        self.pb_radial_cut=False
         #self.wcs=None
         
         if (cube != None)&(pb==None)&(cube_flat==None):
@@ -183,11 +189,25 @@ class pymakeplots:
         :return: (ndarray) mask to apply to the un-clipped cube
         """
         sigma = self.smoothmask_spatial * self.bmaj / self.cellsize
-        smooth_cube = ndimage.uniform_filter(cube, size=[sigma, sigma,4], mode='constant')  # mode='nearest'
+        smooth_cube = ndimage.uniform_filter(cube, size=[sigma, sigma,self.smoothmask_velocity], mode='constant')  # mode='nearest'
         newrms= self.rms_estimate(smooth_cube,0,1) 
-        self.cliplevel=self.rms*self.rmsfac 
+        self.cliplevel=self.rms*self.rmsfac
+        
+        if self.pb_radial_cut or self.pbcliplevel!=None:
+            np.seterr(all='ignore')
+            pb=np.divide(self.flat_cube_trim,self.pbcorr_cube_trim)#,where=self.pbcorr_cube_trim!=0)
+         
         self.maskcliplevel=newrms*self.rmsfac   
-        mask=(smooth_cube > self.maskcliplevel)
+        
+        if self.pb_radial_cut:
+            mask=(smooth_cube > np.divide(self.maskcliplevel,np.abs(pb),where=pb!=0))
+        else:
+            mask=(np.abs(smooth_cube) > self.maskcliplevel)
+            
+            
+        
+        if self.pbcliplevel!=None:
+            mask[pb<self.pbcliplevel]=False
         
         if self.suppress_subbeam_artifacts:
             label,cnt=ndimage.label(mask)#.sum(axis=2))
@@ -195,6 +215,52 @@ class pymakeplots:
             beampix=(self.bmaj*self.bmin)/(self.cellsize**2)
             for thelabel in lab[0:-1][hist<(beampix*self.suppress_subbeam_artifacts)]:
                 mask[label == thelabel]=False
+        #maskorig=mask.copy()
+        if self.masksmoothing>0:
+            expand_by_npix=self.masksmoothing
+            print(expand_by_npix)
+            # structure = np.zeros([3, expand_by_npix * 2 + 1, expand_by_npix * 2 + 1])
+            # Y, X = np.ogrid[:expand_by_npix * 2 + 1, :expand_by_npix * 2 + 1]
+            # R = np.sqrt((X - expand_by_npix) ** 2 + (Y - expand_by_npix) ** 2)
+            # structure[1, :] = R <= expand_by_npix
+            # mask = ndimage.binary_dilation(mask, iterations=1, structure=structure)
+            #breakpoint()
+            mask = ndimage.binary_dilation(mask, iterations=expand_by_npix,axes=(0,1,2))
+            
+            '''
+            r=np.linspace(1,0,self.masksmoothing+1,endpoint=False)[1:]
+            facs=np.exp(-((r-1)**2/(2*(0.33)**2)))
+            
+            maskorig=mask.copy()
+            struct1 = ndimage.generate_binary_structure(2, 1)
+            for i,fac in enumerate(facs):
+                mask2 = ndimage.grey_dilation(maskorig.astype(float), (int(i+1),int(i+1),0), mode='constant')  #
+                mask=np.fmax(mask,mask2*facs[i])
+            '''
+            #
+            #
+            #from kinms import KinMS
+            #from astropy.convolution import convolve
+            #psf=KinMS.makebeam(1,32, 32, [self.masksmoothing,self.masksmoothing,0])
+            
+            #for i in range(0,mask.shape[2]):
+            #    mask[:, :, i] = convolve(mask[:, :, i], psf) #binary
+            #mask=mask.astype(float)    
+            #for i in range(0,mask.shape[2]):    
+            #    mask[:, :, i] = convolve(mask[:, :, i], psf) #smooth
+            #mask[mask<maskorig]=maskorig[mask<maskorig]    
+            #mask=np.fmax(mask,maskorig)    
+        #mask = ndimage.uniform_filter(mask.astype(float), size=[self.masksmoothing,self.masksmoothing,0], mode='constant')  #
+            #print(mask.sum())
+            
+            
+            
+            #mask = ndimage.gaussian_filter(mask.astype(float), [self.masksmoothing,self.masksmoothing,0], mode='constant')  #
+            #if self.maskdilating != 0:
+            #    mask=ndimage.grey_dilation(mask.astype(float), size=(np.round(self.maskdilating).astype(int),np.round(self.maskdilating).astype(int),0))
+
+        
+        #breakpoint()
         
         return mask      
 
@@ -366,6 +432,7 @@ class pymakeplots:
         hdr=scube.header
         cube = np.squeeze(scube.filled_data[:,:,:].T).value #squeeze to remove singular stokes axis if present
         cube[np.isfinite(cube) == False] = 0.0
+        
         try:
             beamtab=scube.beam
         except:
@@ -377,7 +444,13 @@ class pymakeplots:
                     beamvals=[scube.header['bmaj'],scube.header['bmin']]
                     beamtab=Beam(major=np.max(beamvals)*u.deg,minor=np.min(beamvals)*u.deg,pa=self.spectralcube.header['bpa']*u.deg)
                 except:
-                    beamtab=False           
+                    beamtab=False   
+                     
+        if beamtab.major.value ==0:
+            ### MeerKAT style beams
+            beamvals=[np.mean([scube.header['bmaj1'],scube.header['bmaj3826']]),np.mean([scube.header['bmin1'],scube.header['bmin3826']])]
+            beamtab=Beam(major=np.max(beamvals)*u.deg,minor=np.min(beamvals)*u.deg,pa=np.mean([scube.header['bpa1'],scube.header['bpa3826']])*u.deg)
+     
         if primary:
             self.spectralcube=scube
             self.repfreq=np.median(self.spectralcube.with_spectral_unit(u.GHz).spectral_axis)
@@ -705,11 +778,14 @@ class pymakeplots:
         
     def add_beam(self,ax):
         aux_tr_box = AuxTransformBox(ax.transData)
-                
+        if self.rotate!=None:
+            rotang=self.rotate
+        else:
+            rotang=0        
         if self.all_axes_physical:
-            aux_tr_box.add_artist(Ellipse((0, 0), width=self.ang2kpctrans(self.bmaj), height=self.ang2kpctrans(self.bmin), angle=self.bpa+90,edgecolor='black',facecolor='none',linewidth=1.5))                 
+            aux_tr_box.add_artist(Ellipse((0, 0), width=self.ang2kpctrans(self.bmaj), height=self.ang2kpctrans(self.bmin), angle=self.bpa+90+rotang,edgecolor='black',facecolor='none',linewidth=1.5))                 
         else:
-            aux_tr_box.add_artist(Ellipse((0, 0), width=self.bmaj, height=self.bmin, angle=self.bpa+90,edgecolor='black',facecolor='none',linewidth=1.5))                 
+            aux_tr_box.add_artist(Ellipse((0, 0), width=self.bmaj, height=self.bmin, angle=self.bpa+90+rotang,edgecolor='black',facecolor='none',linewidth=1.5))                 
         box = AnchoredOffsetbox(child=aux_tr_box, loc='lower left', pad=0.5, borderpad=0.4,frameon=False)
         ax.add_artist(box)                     
 
@@ -761,7 +837,31 @@ class pymakeplots:
 
         rotmat=np.array([[np.cos(np.deg2rad(self.rotate)),-np.sin(np.deg2rad(self.rotate))],[np.sin(np.deg2rad(self.rotate)),np.cos(np.deg2rad(self.rotate))]])
         dx1,dx2=np.dot(rotmat,np.array([0,length2use]))
-        aux_tr_box.add_artist(Arrow(0, 0,dx1,dx2,color='k'))
+        if (dx1 <0)&(dx2<0):
+            #lower left quadrant
+            startx,starty= np.abs(dx1), np.abs(dx2)
+            endx,endy=0,0
+            ha='right'
+        if (dx1 <0)&(dx2>0):
+            #upper left quadrant
+            startx,starty= 0,0
+            endx,endy= dx1,dx2 
+            ha='right'  
+        if (dx1 >0)&(dx2>0):
+            #upper right quadrant
+            startx,starty= 0,0
+            endx,endy= dx1, dx2
+            ha='left'
+        if (dx1 >0)&(dx2<0):
+            #lower right quadrant
+            startx,starty= -np.abs(dx1), np.abs(dx2)    
+            endx,endy=0,0
+            ha='left'
+            
+        aux_tr_box.add_artist(Text(endx,endy,'N',color='k',ha=ha,fontsize='small',va='center'))
+        aux_tr_box.add_artist(FancyArrowPatch((startx,starty), (endx,endy),
+                                         mutation_scale=100,color='k',arrowstyle='->,head_length=0.1, head_width=0.05'))
+                                         
         box = AnchoredOffsetbox(child=aux_tr_box, loc=loc, frameon=False)
         ax.add_artist(box)
         #ax.text(3, y + 0.05, bracketstyle, ha="center", va="bottom", fontsize=14)   
@@ -1139,9 +1239,10 @@ class pymakeplots:
         centpix_y=np.where(np.isclose(self.yc,0.0,atol=self.cellsize/1.9))[0]
         
 
-
-        rotcube= rotateImage(self.pbcorr_cube_trim*self.mask_trim,90-self.posang,[centpix_x[0],centpix_y[0]])
-
+        if self.posang!=0:
+            rotcube= rotateImage(self.pbcorr_cube_trim*self.mask_trim,90-self.posang,[centpix_x[0],centpix_y[0]])
+        else:
+            rotcube=self.pbcorr_cube_trim*self.mask_trim
 
         pvd=rotcube[:,np.array(rotcube.shape[1]//2-self.pvdthick).astype(int):np.array(rotcube.shape[1]//2+self.pvdthick).astype(int),:].sum(axis=1)
         
@@ -1227,14 +1328,17 @@ class pymakeplots:
         
         mask2d=self.mask_trim.sum(axis=2).reshape((self.mask_trim.shape[0],self.mask_trim.shape[1],1)).astype(bool)
         mask2d=ndimage.binary_dilation(mask2d,iterations=2)
-        spec=(self.pbcorr_cube[self.spatial_trim[0]:self.spatial_trim[1],self.spatial_trim[2]:self.spatial_trim[3],:]*mask2d).sum(axis=0).sum(axis=0)
-        
+        if self.bunit == "K":
+            spec=np.nanmean(self.pbcorr_cube[self.spatial_trim[0]:self.spatial_trim[1],self.spatial_trim[2]:self.spatial_trim[3],:],axis=(0,1))*1e3
+            spec_mask=np.nanmean((self.pbcorr_cube_trim*self.mask_trim),axis=(0,1))*1e3
+        else:
+            spec=(self.pbcorr_cube[self.spatial_trim[0]:self.spatial_trim[1],self.spatial_trim[2]:self.spatial_trim[3],:]*mask2d).sum(axis=0).sum(axis=0)
+            spec_mask=(self.pbcorr_cube_trim*self.mask_trim).sum(axis=0).sum(axis=0)
 
-        spec_mask=(self.pbcorr_cube_trim*self.mask_trim).sum(axis=0).sum(axis=0)
+        
         ylab="Unknown"
         
         if (''.join(self.bunit.split())).lower() == "Jy/beam".lower():
-            
             spec*=1/self.beam_area()
             spec_mask*=1/self.beam_area()
             
@@ -1245,7 +1349,7 @@ class pymakeplots:
             else:
                 ylab="Flux Density (Jy)"
         if self.bunit == "K":
-            ylab="Brightness Temp. (K)"
+            ylab="Brightness Temp. (mK)"
             
         if nsum:
             spec=np.append(running_mean(spec,nsum),spec[-1])

{pymakeplots-0.2.4.dist-info → pymakeplots-0.2.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pymakeplots
-Version: 0.2.4
+Version: 0.2.6
 Home-page: https://github.com/TimothyADavis/pymakeplots
 Author: Timothy A. Davis
 Author-email: DavisT@cardiff.ac.uk
@@ -19,6 +19,9 @@ Requires-Dist: spectral-cube
 Requires-Dist: radio-beam
 Requires-Dist: pafit
 
+# pymakeplots
+<img style="float:top,right" src="https://github.com/TimothyADavis/pymakeplots/blob/master/NGC1684_allplots.png">
+
 [![Python 3.8](https://img.shields.io/badge/python-3.8-blue.svg)](https://www.python.org/downloads/release/python-382/) [![PyPI version](https://badge.fury.io/py/pymakeplots.svg)](https://badge.fury.io/py/pymakeplots) 
 
 A python module for making publication quality plots and output datafiles (including moment zero, one, two, PVD's and spectra) from interferometric datacubes. 

pymakeplots-0.2.6.dist-info/RECORD

@@ -0,0 +1,9 @@
+pymakeplots/__init__.py,sha256=PLKnIm6rIKYjH_b6L9UBCFtv1lKt5GItdBKDbSOhuMU,87
+pymakeplots/pymakeplots.py,sha256=pnPm6IBGsydY5QTYdmmpqdZnznR7kyt_e_5DYVwQ0Fw,56827
+pymakeplots/sauron_colormap.py,sha256=8APka-_L432wyICcHcySjk3qmjNOynb3iDjjlMuUTU0,4448
+pymakeplots-0.2.6.dist-info/LICENSE.md,sha256=qtvmvajOPCad_5HMY5u49hldzBIXz7tbHbuGSG_HE5o,1077
+pymakeplots-0.2.6.dist-info/METADATA,sha256=SiNH7cgb8pdcm6GEUeLDTJJjYcI7fRBIEkWuqDnUwaA,1976
+pymakeplots-0.2.6.dist-info/WHEEL,sha256=Z4pYXqR_rTB7OWNDYFOm1qRk0RX6GFP2o8LgvP453Hk,91
+pymakeplots-0.2.6.dist-info/top_level.txt,sha256=KgG17vI_D6BsiKRe_81UU5709tXc6Ha7gx1IwjA7ur8,12
+pymakeplots-0.2.6.dist-info/zip-safe,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
+pymakeplots-0.2.6.dist-info/RECORD,,

pymakeplots-0.2.4.dist-info/RECORD

@@ -1,9 +0,0 @@
-pymakeplots/__init__.py,sha256=PLKnIm6rIKYjH_b6L9UBCFtv1lKt5GItdBKDbSOhuMU,87
-pymakeplots/pymakeplots.py,sha256=qDG7pwhiUprjVvSqQzPt6PyU-W_BJGGf-pZTsN3kK6U,52065
-pymakeplots/sauron_colormap.py,sha256=8APka-_L432wyICcHcySjk3qmjNOynb3iDjjlMuUTU0,4448
-pymakeplots-0.2.4.dist-info/LICENSE.md,sha256=qtvmvajOPCad_5HMY5u49hldzBIXz7tbHbuGSG_HE5o,1077
-pymakeplots-0.2.4.dist-info/METADATA,sha256=7IC9lbVFzP8BVTdzsci1b7w1T39TytxqVyNWmk-9TAE,1847
-pymakeplots-0.2.4.dist-info/WHEEL,sha256=Z4pYXqR_rTB7OWNDYFOm1qRk0RX6GFP2o8LgvP453Hk,91
-pymakeplots-0.2.4.dist-info/top_level.txt,sha256=KgG17vI_D6BsiKRe_81UU5709tXc6Ha7gx1IwjA7ur8,12
-pymakeplots-0.2.4.dist-info/zip-safe,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
-pymakeplots-0.2.4.dist-info/RECORD,,