lgtm linting in progress

ImageD11src/ImageD11_thread.py

@@ -26,7 +26,7 @@
     import queue as Queue 
 
 import threading
-global stop_now
+# global stop_now
 stop_now = False
 
 class ImageD11_thread(threading.Thread):

ImageD11src/blobcorrector.py

@@ -50,7 +50,6 @@ def readfit2dfloats(filep, nfl):
             i = i + 14
             if j == nfl: 
                 break
-        i = i + 1
     return ret
 
 class correctorclass: #IGNORE:R0902
@@ -197,8 +196,8 @@ def readfit2dspline(self, name):
         if myline[:7] != "SPATIAL":
             raise SyntaxError(name + \
                 ": file does not seem to be a fit2d spline file")
-        myline = fin.readline() # BLANK LINE
-        myline = fin.readline() # VALID REGION
+        fin.readline() # BLANK LINE
+        fin.readline() # VALID REGION
         myline = fin.readline() # the actual valid region, 
                                # assuming xmin,ymin,xmax,ymax
         logging.debug("xmin,ymin,xmax,ymax, read: "+myline)
@@ -210,8 +209,8 @@ def readfit2dspline(self, name):
         logging.debug("gridspace, xsize, ysize: "+myline)
         self.gridspacing, self.xsize, self.ysize = \
          [float(z) for z in  myline.split()]
-        myline = fin.readline() # BLANK
-        myline = fin.readline() # X-DISTORTION
+        fin.readline() # BLANK
+        fin.readline() # X-DISTORTION
         myline = fin.readline() # two integers nx1,ny1
         logging.debug("nx1, ny1 read: "+myline)
         nx1, ny1 = [int(z) for z in myline.split()]
@@ -220,8 +219,8 @@ def readfit2dspline(self, name):
         ty1 = numpy.array(readfit2dfloats(fin, ny1), numpy.float32)
         cf1 = numpy.array(readfit2dfloats(fin, (nx1 - 4) * (ny1 - 4)),  
                           numpy.float32)
-        myline = fin.readline() #BLANK
-        myline = fin.readline() # Y-DISTORTION
+        fin.readline() #BLANK
+        fin.readline() # Y-DISTORTION
         myline = fin.readline() # two integers nx2, ny2
         nx2 , ny2 = [int(z) for z in myline.split()]
         tx2 = numpy.array(readfit2dfloats(fin, nx2), numpy.float32)

ImageD11src/correct.py

@@ -59,6 +59,7 @@ def correct(data_object,
         # direction of a previously radially transformed image
         # Gives the liquid contribution
         med = numpy.median( picture )
+        # FIXME
         if True: # Suboption - save the median or not?
             obj = fabio.deconstruct_filename( data_object.header['filename'] )
             obj.extension = ".bkm"

ImageD11src/eps_sig_solver.py

@@ -219,7 +219,7 @@ def compute_write_eps_sig(self,outputfile):
                 except:
                     print("couldn't compute stress! please check the crystal_symmetry parameters and elastic constants")
                     writestress = False
-                    pass
+
 
                 ''' writing down the results'''
 

ImageD11src/fft_index_refac.py

@@ -297,21 +297,21 @@ def slow_score(self):
 
 
 
-        sm = np.zeros( (len(diff), len(diff)), np.float)
-        for k in range(len(diff)):
-            i = order[k]
-            sm[i,i] = np.dot(diff[i], diff[i])
-        for k in range(len(diff)-1):
-            i = order[k]
-            for l in range(i+1, len(diff)):
-                j = order[l]
-                sm[i,j] = np.dot(diff[i],diff[j])/sm[i,i]/sm[j,j]
-                sm[j,i] = sm[i,j]
-        for i in range(len(diff)):
-            sm[i,i] = 1.
-        print(sm[:5,:5])
-        print("Scoring takes",time.time()-start)
-        return sm
+        # sm = np.zeros( (len(diff), len(diff)), np.float)
+        # for k in range(len(diff)):
+        #     i = order[k]
+        #     sm[i,i] = np.dot(diff[i], diff[i])
+        # for k in range(len(diff)-1):
+        #     i = order[k]
+        #     for l in range(i+1, len(diff)):
+        #         j = order[l]
+        #         sm[i,j] = np.dot(diff[i],diff[j])/sm[i,i]/sm[j,j]
+        #         sm[j,i] = sm[i,j]
+        # for i in range(len(diff)):
+        #     sm[i,i] = 1.
+        # print(sm[:5,:5])
+        # print("Scoring takes",time.time()-start)
+        # return sm
 
 #####
 #        To Do

ImageD11src/indexer.py

@@ -69,7 +69,7 @@ def updatecolfile(self):
             elif "xc" in self.cf.titles: 
                 pks = self.cf.xc, self.cf.yc
             else:
-                raise "peaks file misses xc or sc"
+                raise Exception("peaks file misses xc or sc")
             xl,yl,zl = transform.compute_xyz_lab( pks,
                                     **self.transformpars.parameters)
             self.cf.addcolumn(xl,"xl")
@@ -132,7 +132,6 @@ def assigntorings(self):
         """
         Assign the g-vectors to hkl rings that are in self.unitcell
         """
-        dsr = self.unitcell.ringds
         self.cf.ring[:]=-1
         self.cf.ringerr[:]=42.
         tol = self.transformpars.get( "fit_tolerance" )

ImageD11src/indexing.py

@@ -540,7 +540,6 @@ def find(self):
         # found=0
         hits=[]
         start = time.time()
-        start=time.time()
         mtol = -tol # Ugly interface - set cosine tolerance negative for all
                     # instead of best
         for i in range(len(i1)):

ImageD11src/peaksearcher.py

@@ -258,13 +258,9 @@ def fso(f0,f1):
     # Make a blobimage the same size as the first image to process
 
 
-    # List comprehension - convert remaining args to floats - must be unique list        
-    thresholds_list = [float(t) for t in options.thresholds]
-    try:
-        thresholds_list = list(set(thresholds_list))
-    except:
-        import sets
-        thresholds_list = list(sets.Set(thresholds_list))
+    # List comprehension - convert remaining args to floats 
+    # must be unique list so go via a set
+    thresholds_list = list( set( [float(t) for t in options.thresholds] ) )
     thresholds_list.sort()
 
     li_objs={} # label image objects, dict of

ImageD11src/refinegrains.py

@@ -235,7 +235,7 @@ def readubis(self, filename):
             print(filename, type(filename))
             raise
         for i, g in enumerate(ul):
-            name = filename + "_" + str(i)
+            # name = filename + "_" + str(i)
             # Hmmm .... multiple grain files?
             name = i
             self.grainnames.append(i)

ImageD11src/rotdex.py

@@ -137,8 +137,7 @@ def fit_ub_t( ub, translation, hkl, peaks_Cxyz, beam_Cxyz, wavelength):
             dg[i+9] = dgobsdt[i]       # translation at 9,10,11
         gcalc =  np.dot( ubnew , hkl ) # 3xn
         gdiff = gcalc - gobs
-        if 0:
-            print((gdiff*gdiff).ravel().sum(),tnew)
+        #    print((gdiff*gdiff).ravel().sum(),tnew)
         dg.shape = 12,3*npk
         mat = np.dot( dg, dg.T )
         rhs = np.dot( dg, gdiff.ravel() )

ImageD11src/rsv.py

@@ -1,5 +1,5 @@
 
-from __future__ import print_function. division
+from __future__ import print_function, division
 
 """
 Reciprocal Space Volume

ImageD11src/silxGui/silx_sptview.py

@@ -84,7 +84,6 @@ def warn(self, message):
         silx.gui.qt.QMessageBox.warning(None, "Warning", message)
 
 if __name__=="__main__":
-    global app
     qapp = silx.gui.qt.QApplication([])
     s=sptview( sys.argv[1] )
     s.window.show()

ImageD11src/sym_u.py

@@ -36,13 +36,11 @@ def m_to_string(m):
     """
     st = []
     for i in range(3):
-        needplus = 0  # ???
         for v,s in zip([ [ 1,0,0] , [ 0,1,0], [0,0,1] ],
                             "xyz"):
             c = np.dot(v,m.T[i])
             if abs(c)>0:
                 st.append( "%s%s"%(fmt(c),s))
-                needplus = 1
         if i<2:
             st.append(",")
     return "".join(st)
@@ -267,8 +265,8 @@ def __init__(self, tol = 1e-5):
         """
         Identity is to not move at all
         """
-        self.group = [ np.zeros(3, np.float) ]
-        self.tol = tol
+        group.__init__(self,tol)
+
     def op(self, x, y):
         """
         Means of generating new thing from two others

ImageD11src/tkGui/twodplot.py

@@ -138,16 +138,16 @@ def keypress(self,*arg):
 
     def bindkeys(self):
         return
-        self.bind_all('<Left>' ,lambda e: self.keypress(self.a.panx,1 )  )
-        self.bind_all('<Right>',lambda e: self.keypress(self.a.panx,-1)  )
-        self.bind_all('<Up>'   ,lambda e: self.keypress(self.a.pany,-1 ) )
-        self.bind_all('<Down>' ,lambda e: self.keypress(self.a.pany,1)   )
-        self.bind_all('<Shift-Left>' ,lambda e: self.keypress(self.a.zoomx,-1 )  )
-        self.bind_all('<Shift-Right>',lambda e: self.keypress(self.a.zoomx,1)  )
-        self.bind_all('<Shift-Up>'   ,lambda e: self.keypress(self.a.zoomy,1 ) )
-        self.bind_all('<Shift-Down>' ,lambda e: self.keypress(self.a.zoomy,-1)   )
-        self.bind_all('<Next>' , lambda e : self.keypress(self.autoscale)   )
-        self.bind_all('<Prior>', lambda e : self.keypress(self.autoscaley, e )  )
+        # self.bind_all('<Left>' ,lambda e: self.keypress(self.a.panx,1 )  )
+        # self.bind_all('<Right>',lambda e: self.keypress(self.a.panx,-1)  )
+        # self.bind_all('<Up>'   ,lambda e: self.keypress(self.a.pany,-1 ) )
+        # self.bind_all('<Down>' ,lambda e: self.keypress(self.a.pany,1)   )
+        # self.bind_all('<Shift-Left>' ,lambda e: self.keypress(self.a.zoomx,-1 )  )
+        # self.bind_all('<Shift-Right>',lambda e: self.keypress(self.a.zoomx,1)  )
+        # self.bind_all('<Shift-Up>'   ,lambda e: self.keypress(self.a.zoomy,1 ) )
+        # self.bind_all('<Shift-Down>' ,lambda e: self.keypress(self.a.zoomy,-1)   )
+        # self.bind_all('<Next>' , lambda e : self.keypress(self.autoscale)   )
+        # self.bind_all('<Prior>', lambda e : self.keypress(self.autoscaley, e )  )
 
     def autoscaley(self,e):
         print(dir(self.a.dataLim))
@@ -215,17 +215,17 @@ def replot(self):
                 self.a.set_title(item.d["title"])
             try:
                 if  "plottype" in item.d:
-                    ret = self.a.hist(item.y,item.x)
+                    self.a.hist(item.y,item.x)
                 elif item.x.shape[0]>self.maxpoints:
                     if self.quiet=="No":
                         if messagebox.askyesno("Slow plotting workaround","Shall I plot only the first %d points for increased speed?"%(self.maxpoints)):
-                            ret = self.a.plot(item.x[:self.maxpoints],item.y[:self.maxpoints],**po)
+                            self.a.plot(item.x[:self.maxpoints],item.y[:self.maxpoints],**po)
                         else:
-                            ret = self.a.plot(item.x,item.y,**po)
+                            self.a.plot(item.x,item.y,**po)
                     else:
-                        ret = self.a.plot(item.x[:self.maxpoints],item.y[:self.maxpoints],**po)
+                        self.a.plot(item.x[:self.maxpoints],item.y[:self.maxpoints],**po)
                 else:
-                    ret = self.a.plot(item.x,item.y,**po)
+                    self.a.plot(item.x,item.y,**po)
             except:
                 print("plotting exception ignored")
                 raise

find_all_files_interfacing.py

@@ -0,0 +1,34 @@
+
+import os
+
+apui = []
+syui = []
+noui = []
+
+root = "."
+for dirName, subdirList, fileList in os.walk(root):
+    if True in [dirName.find(s)>=0 for s in ("__","build",".git",".vscode") ]:
+        continue
+    for f in fileList:
+        if f.endswith(".py"):
+            p = os.path.join(dirName, f)
+            s = open( p , "r" ).read()
+            if "optparse" in s or "add_option" in s:
+                apui.append( p )
+            elif "argv" in s:
+                syui.append( p )
+            else:
+                noui.append( p )
+
+print("Neither:")
+for f in noui:
+    print(f)
+
+
+print("argv:")
+for f in syui:
+    print(f)    
+
+print("optparse:")
+for f in apui:
+    print(f)

lgtm.yml

@@ -6,4 +6,3 @@ extraction:
   python:
     python_setup:
       version: 3
-

sandbox/CRL.py

@@ -248,7 +248,7 @@
 #    x^2 + y^2 = 2*Ry
 # ... x>>y : x^2 = 2Ry
 # so Y = x^2/(2R)
-x = np.linspace( -.5e-3, .5e-3, 100)
+#x = np.linspace( -.5e-3, .5e-3, 100)
 x = np.linspace( -25e-6, 25e-6, 100)
 #pl.plot( 1e6*x, 1e6*x*x/(2*R_SI), "-" )
 E = 40 

sandbox/abonnin/make_point_sino.py

@@ -91,13 +91,13 @@ def fit_sino( omega, obs, debug=False ):
         print("#  spot3d_id  omega  xpos  intensity")
         for i in range(len(usedpks)):
             print("%-7d  %8.1f %9.5f %15g"%(usedpks[i], omused[i], xposused[i], intens[i]))
-        if 0:
-            pl.clf()
-            pl.title("Grain number %d"%(ng))
-            pl.plot(om, xpos,"o")
-            pl.plot(omused, xposused,"o")
-            pl.plot(omused, calc,"+")
-            pl.ion()
-            pl.show()
-            pl.savefig("grainfit_%d.png"%(ng))
+        # if 0:
+        #     pl.clf()
+        #     pl.title("Grain number %d"%(ng))
+        #     pl.plot(om, xpos,"o")
+        #     pl.plot(omused, xposused,"o")
+        #     pl.plot(omused, calc,"+")
+        #     pl.ion()
+        #     pl.show()
+        #     pl.savefig("grainfit_%d.png"%(ng))
         ng += 1

sandbox/art.py

@@ -1,5 +1,5 @@
 
-from __future__ import print_function
+from __future__ import print_function, division
 
 
 """
@@ -57,7 +57,7 @@ def update_wtd( recon, proj, angle, msk, dbg=True ):
     cImageD11.put_incr( npcalc_proj, idx_hi, wt_hi )
     cImageD11.put_incr( npcalc_proj, idx_lo, wt_lo )
     npcalc_proj = np.where(npcalc_proj >0 ,npcalc_proj, 1)
-    update =  np.zeros( r.shape, np.float32)
+    # update =  np.zeros( r.shape, np.float32)
     update =  wt_hi*np.take( error/npcalc_proj, idx_hi ) 
     update += wt_lo*np.take( error/npcalc_proj, idx_lo )    
 
@@ -78,7 +78,7 @@ def update_wtd( recon, proj, angle, msk, dbg=True ):
     #pl.colorbar()
     #pl.show()
 
-    update = update 
+    # update = update 
     update.shape = recon.shape
     print(update.sum(),error.sum(), end=' ')
     if dbg:

sandbox/cleanbg.py

@@ -1,5 +1,5 @@
 
-from __future__ import print_function
+from __future__ import print_function, division
 #!/usr/bin/python2.7
 
 import numpy as np, fabio
@@ -43,7 +43,7 @@ def cleanbg( stem, nimages, newstem ):
        print(i,name)
    bg = np.clip( buffy.min( axis = 0 ), 90, 65535 ) - 90
    # Deal with images up to bufsize/2
-   for i in range(bufsize/2):
+   for i in range(bufsize//2):
        outname = newstem + "%04d.edf"%(i)
        print("write",outname, buffo[i].name)
        np.subtract( buffo[i].data , bg, buffo[i].data )
@@ -64,15 +64,15 @@ def cleanbg( stem, nimages, newstem ):
        buffy[bp] = o.data.copy()
        bg = np.clip( buffy.min( axis = 0 ), 90, 65535 ) - 90
        # Out image is i - bufsize/2
-       op = (i-bufsize/2-1)%bufsize
+       op = (i-bufsize//2-1)%bufsize
        np.subtract( buffo[op].data , bg, buffo[op].data )
        outname = newstem + "%04d.edf"%(i-bufsize/2-1)
        print(i,outname, buffo[op].name)
        buffo[op].write( outname )
    n=i
-   for i in range(bufsize/2):
+   for i in range(bufsize//2):
        outname = newstem + "%04d.edf"%(n+i-bufsize/2)
-       bp = (n+i-bufsize/2)%bufsize
+       bp = (n+i-bufsize//2)%bufsize
        print("write",outname, buffo[bp].name)
        np.subtract( buffo[bp].data , bg, buffo[bp].data )
        buffo[bp].write( outname )

sandbox/indexer.py

@@ -67,7 +67,7 @@ def updatecolfile(self):
           elif "xc" in self.cf.titles: 
              pks = self.cf.xc, self.cf.yc
           else:
-             raise "peaks file misses xc or sc"
+             raise Exception("peaks file misses xc or sc")
           xl,yl,zl = transform.compute_xyz_lab( pks,
                                                 **self.transformpars.parameters)
           self.cf.addcolumn(xl,"xl")