flake8 preparation and ci fixes

ImageD11/blobcorrector.py

@@ -280,8 +280,8 @@ def __init__(self,
         assert self.dx.shape == self.dy.shape
 
     def __call__(self, pks):
-        si = np.round(pks['s_raw']).astype(int)
-        fi = np.round(pks['f_raw']).astype(int)
+        si = numpy.round(pks['s_raw']).astype(int)
+        fi = numpy.round(pks['f_raw']).astype(int)
         pks['fc'] = self.dx[ si, fi ] + pks['f_raw']
         pks['sc'] = self.dy[ si, fi ] + pks['s_raw']
         return pks

ImageD11/compute_fazit.py

@@ -50,7 +50,7 @@ def __init__(self, splinefile = None,
         for key in self.required_pars:
 
             if key not in self.pars.parameters:
-                raise Exception("Missing parameter "+str(par))
+                raise Exception("Missing parameter "+str(key))
 
     def compute_tth_eta(self, dims):
         """

ImageD11/fft_index_refac.py

@@ -344,7 +344,7 @@ def test(options):
     #sys.stdout.flush()
     #ubinew = go.reduce(go.UBIALL)
     #print "After reduction", len(ubinew)
-    go.UBIALL = ubinew
+    #go.UBIALL = ubinew
     go.slow_score()
     #from matplotlib.pylab import imshow, show
     #imshow(im)

ImageD11/project/h5demo1.py

@@ -84,4 +84,4 @@ def writesino(h5name, omegas, dtys, filenames):
         else:
             print('debug please')
             print(fab.shape,fab)
-            print(h5v.shape,h5e)
+            print(h5v.shape,h5v)

ImageD11/project/project.py

@@ -35,8 +35,8 @@ class Scan( object ):
     edges = which nodes are adjacent to this node
     """
     def __init__(self,
-                 nodes = None,    # type: List[]
-                 edges = None,    # type: List[[int,]]
+                 nodes = None,    # a List[]
+                 edges = None,    # a List[[int,]]
                  ):      
         """
         nodes = measurement points in the scan
@@ -96,9 +96,9 @@ def neighbors( self, node ):
         node = scan point (Image, Omega, etc)
         node = integer
         """
-        if isinstance( i, int ):
-            return self.edges[i]
-        if isinstance( i, tuple): 
+        if isinstance( node, int ):
+            return self.edges[node]
+        if isinstance( node, tuple): 
             i = self.node_index[ node ]
             return self.edges[i]
         raise TypeError("node not understood, want tuple or int row index")
@@ -211,8 +211,8 @@ def mergeScans( scan1, scan2 ):
     n2 = len(scan2)
     # "+" joins lists:
     nodes = scan1.nodes + scan2.nodes
-    edges = scan1.edges + [ (i + n1, j + n1) for i,j in edges ]
-    return Scan( nodes, edge )
+    edges = scan1.edges + [ (i + n1, j + n1) for i,j in nodes ]
+    return Scan( nodes, edges )
 
 
 class Project( object ):

ImageD11/saintraw.py

@@ -177,7 +177,7 @@ def parsedocs(self):
         Parse the saint documentation for the Bruker format
         """
         self.titles = []
-        title = None
+        title = help = format = None
         for line in self.doc.split("\n"):
             if len(line.rstrip()) == 0:
                 if title is not None:

ImageD11/sparseframe.py

@@ -167,8 +167,8 @@ def to_hdf_group( frame, group ):
                                    dtype=px.dtype,
                                    **opts ) 
             group[pxname][:] = px
-            if pxname in self.meta:
-                group[pxname].attrs = dict( self.meta[pxname] )
+            if pxname in frame.meta:
+                group[pxname].attrs = dict( frame.meta[pxname] )
 
 
 class SparseScan( object ):

ImageD11/tkGui/twodplot.py

@@ -341,10 +341,10 @@ def on_up(self,event):
     import numpy as np
     from math import pi
     x=np.arange(0.0,3.0,0.01)
-    dat=epffile.powderdata(x,
-                           np.sin(2*pi*x)+5,
-                           np.sqrt(sin(2*pi*x)+5),
-                           { "title":"sin x" })
+    dat=data(x,
+             np.sin(2*pi*x)+5,
+             np.sqrt(np.sin(2*pi*x)+5),
+             { "title":"sin x" })
 
     root = Tk.Tk()
     root.wm_title("Two dimensional plotting")

ImageD11/transform.py

@@ -216,7 +216,7 @@ def sinth2_sqrt_deriv(xyz):
     x,y,z = xyz
     R = z*z + y*y
     Q = R + x*x
-    SQ = sqrt(Q)
+    SQ = np.sqrt(Q)
     R2 = R/2
     # at x==y==0 this is undefined. ac
     rQ_xSQ = 1/(Q + x*SQ)
@@ -686,9 +686,10 @@ def __init__( self, pars ):
             self.sc = slow + self.ds
             self.fc = fast + self.df
         elif 'spline' in pars: # need to test this...
+            from ImageD11 import blobcorrector
             b = blobcorrector.correctorclass( self.pars['spline'] )
             s = int(b.ymax - b.ymin), int(b.xmax - b.xmin)
-            if shape in self.pars:      # override. Probabl
+            if 'shape' in self.pars:      # override. Probabl
                 s = self.pars['shape'] 
             self.shape = s
             self.fc, self.sc = b.make_pixel_lut( s ) 

sandbox/abonnin/fix_omega_angles.py

@@ -1,4 +1,5 @@
 from ImageD11.columnfile import columnfile
+from pylab import plot
 c = columnfile("mainphase.flt")
 c.addcolumn(c.omega.copy(), "image_number")
 c.omega[:] = (c.image_number/147).astype(int)

sandbox/abonnin/make_point_sino.py

@@ -1,7 +1,7 @@
 
 from __future__ import print_function
 
-import numpy as np
+import numpy as np, pylab as pl
 
 
 def read_log(fname):

sandbox/bravias.py

@@ -55,20 +55,20 @@ def ferraris_and_ivaldi(ubi, tol = 0.001):
     Tolerance is for grouping vector lengths.
     """
     cpar = ubitocellpars(ubi)
-    cell = unitcell( cp )
+    cell = unitcell( cpar )
     dlim = cell.ds( np.array( [7,7,7] ))
-    u.makerings( dlim , tol)
+    cell.makerings( dlim , tol)
     mult = [ len(cell.ringhkls[d]) for d in cell.ringds ]
     mx = max(mult)
     mn = min(mult)
     cases = {
         (2,  2) : fi_triclinic,
         (4,  2) : fi_monoclinic,
-        (8,  2) : fi_orthorhombic,
-        (12, 2) : fi_rhombohedral,
-        (16, 2) : fi_tetragonal,
-        (24, 2) : fi_hexagonal,
-        (48, 2) : fi_cubic
+#        (8,  2) : fi_orthorhombic,
+#        (12, 2) : fi_rhombohedral,
+#        (16, 2) : fi_tetragonal,
+#        (24, 2) : fi_hexagonal,
+#        (48, 2) : fi_cubic
     }
 
 def vecang( v1, v2 ):

sandbox/ev78/integrate_them.py

@@ -43,9 +43,9 @@ def edffilenameseries(stem, first=None, last=None, glob=False, extn=".edf"):
     """
     if glob:
         import glob, os
-	files = glob.glob("%s*%s"%(stem,extn))
+        files = glob.glob("%s*%s"%(stem,extn))
         filesdone = glob.glob("%s*%s"%(stem,".dat"))
-	filesdone = [f.replace(".dat",extn) for f in filesdone]
+        filesdone = [f.replace(".dat",extn) for f in filesdone]
         for f in files:
             if f not in filesdone:
                 yield f
@@ -382,16 +382,6 @@ def check_pars( o ):
 
 
 
-def polstuff():
-    # Now look for the polarisation component
-    stth = numpy.sin(integrator.twoThetaArray(data.shape))
-    cchi = numpy.cos( integrator.chiArray(data.shape)*2 )
-    pfac = cchi*stth*stth
-    #print p.min(),p.max(),stth.min(),stth.max()
-    #numpy.divide( calcimage, p , calcimage )
-    t.bench("computed image")
-    poldifference = (data - calcimage)*mask*pfac
-
 
 if __name__ == "__main__":
     from optparse import OptionParser

sandbox/ev78/makevols.py

@@ -10,7 +10,7 @@ def readtxt(fname):
     Reads txt file written by spec and fills in table of:
       filenumber, diffty, diffrz, pico3, current
     """
-    cnext = None
+    cnext = cindex = None
     h = {}
     vals = []
     ctrs = "diffty pico3 notsrcu".split()

sandbox/find_pseudo_twins.py

@@ -54,7 +54,7 @@
 
 tol = 2.35*angtol*np.pi/180.0
 tol2 = tol*tol
-print "#",
+print( "#", end = ' ')
 for i,g1 in enumerate(gl):
     np.dot( g1.ub, hkls, out=gv1 )
     for j in range(i+1, len(gl)):
@@ -80,22 +80,22 @@
             dist = np.sqrt( ((g1.translation-g2.translation)**2).sum() )
             if dist > 500:
                 continue
-            print "\n# grains %d %d  frac %.3f scor %.3f"%(i,j,tscor,scor.sum()),
+            print("\n# grains %d %d  frac %.3f scor %.3f"%(i,j,tscor,scor.sum()),end=' ')
             rotangs = xfab.symmetry.Umis( g1.u, g2.u, 7 )
             angs = [a[1] for a in rotangs]
             dist = np.sqrt( ((g1.translation-g2.translation)**2).sum() )
-            print " misori %.3f  dist %.1f"%(np.min(angs), dist)
-            print "# g1.t % 7.3f % 7.3f % 7.3f"%tuple(g1.translation)
-            print "# g2.t % 7.3f % 7.3f % 7.3f"%tuple(g2.translation)
-            print "# i (h k l) -> (h k l)  Angle  Scor "
+            print(" misori %.3f  dist %.1f"%(np.min(angs), dist))
+            print("# g1.t % 7.3f % 7.3f % 7.3f"%tuple(g1.translation))
+            print("# g2.t % 7.3f % 7.3f % 7.3f"%tuple(g2.translation))
+            print("# i (h k l) -> (h k l)  Angle  Scor ")
             ip = 0
             order = np.argsort(scor)
             for k in order[::-1]:
                 if scor[k] > 0.001:
                     h1,k1,l1 = hkls.T[k]
                     h2,k2,l2 = hklr.T[k]
                     ip += 1
-                    print "%d ( % d % d % d ) -> ( % .3f % .3f % .3f ) %.3f %.5f"%( ip,
-                        h1,k1,l1,  h2,k2,l2,  np.degrees(np.sqrt(angerr2[k])),scor[k])
-            print "#",
+                    print( "%d ( % d % d % d ) -> ( % .3f % .3f % .3f ) %.3f %.5f"%( ip,
+                        h1,k1,l1,  h2,k2,l2,  np.degrees(np.sqrt(angerr2[k])),scor[k]))
+            print("#",end=' ')
 

sandbox/grid_index.py

@@ -91,7 +91,7 @@ def domap(  OmFloat,  OmSlop,
         o.scandata["internal"] = colfile
         o.tolerance = tol
         o.readubis( grainsfile )
-        if symmetry is not "triclinic":
+        if symmetry != "triclinic":
             o.makeuniq( symmetry )
         o.generate_grains()
         o.refinepositions()

sandbox/newpeaksearch3d.py

@@ -169,7 +169,7 @@ def dict_to_colfile( c ):
     colf.set_bigarray( [ c[t] for t in titles ] )
     return colf
 
-
+# /data/id11/jon/inhouse/jon/mar10/segment2d
 hdffile = "fe3o4_peaks.hdf"
 folder = "entry"
 parfile = "avg.par"