Commit adab0a7f authored by christoph's avatar christoph
Browse files

small bug fixes

parent 5a39cd57
...@@ -1975,7 +1975,7 @@ class roi_finder: ...@@ -1975,7 +1975,7 @@ class roi_finder:
ax1.legend(['Row No. %02d / %02d' %(1, rw_data[roi_keys[0]].shape[1])], ax1.legend(['Row No. %02d / %02d' %(1, rw_data[roi_keys[0]].shape[1])],
frameon=False, loc=1, fontsize='x-small') frameon=False, loc=1, fontsize='x-small')
# plot the very first mask image # plot the very first mask image
ax2.plot([-0.5, data_dict_norm['ROI00'].shape[0]+0.5, data_dict_norm['ROI00'].shape[0]+0.5, -0.5], ax2.plot([-0.5, data_dict_norm['ROI00'].shape[2]+0.5, data_dict_norm['ROI00'].shape[2]+0.5, -0.5],
[-0.5, -0.5, 0.5, 0.5 ], 'k-') [-0.5, -0.5, 0.5, 0.5 ], 'k-')
ax2.imshow( np.sum(data_dict_norm['ROI00'], axis=0), interpolation=interpolation, cmap=cmap ) ax2.imshow( np.sum(data_dict_norm['ROI00'], axis=0), interpolation=interpolation, cmap=cmap )
ax2.imshow( red_rois_copy[roi_keys[0]][1], interpolation=interpolation, cmap='Greys', alpha=0.5 ) ax2.imshow( red_rois_copy[roi_keys[0]][1], interpolation=interpolation, cmap='Greys', alpha=0.5 )
......
...@@ -2371,11 +2371,11 @@ def vaspBoxParser(filename): ...@@ -2371,11 +2371,11 @@ def vaspBoxParser(filename):
for ind in range(num_atoms[zz]): for ind in range(num_atoms[zz]):
# print(ind, kind, cou) # print(ind, kind, cou)
rel_coords = np.array([float(ii) for ii in all_lines[coor_start+cou].split()]) rel_coords = np.array([float(ii) for ii in all_lines[coor_start+cou].split()])
abs_coords = cell.dot(rel_coords) abs_coords = cell.T.dot(rel_coords)
atoms.append(xyzAtom(kind, abs_coords, cou )) atoms.append(xyzAtom(kind, abs_coords, cou ))
cou += 1 cou += 1
box = xyzBox(atoms,boxLength=0.0) box = xyzBox(atoms,boxLength=0.0)
box.lattice = np.array([cell1, cell2, cell3]) box.lattice = np.array([cell1, cell2, cell3]).T
box.lattice_inv = np.linalg.inv(box.lattice) box.lattice_inv = np.linalg.inv(box.lattice)
return box return box
...@@ -2409,7 +2409,7 @@ def vaspTrajecParser(filename, min_boxes=0, max_boxes=1000): ...@@ -2409,7 +2409,7 @@ def vaspTrajecParser(filename, min_boxes=0, max_boxes=1000):
atoms.append(xyzAtom( ([atom_kinds[ii_kind]]*num_atoms[ii_kind])[jj_num] ,coordinates[coorcou],counter)) atoms.append(xyzAtom( ([atom_kinds[ii_kind]]*num_atoms[ii_kind])[jj_num] ,coordinates[coorcou],counter))
coorcou += 1 coorcou += 1
box = xyzBox(atoms,boxLength=0.0) box = xyzBox(atoms,boxLength=0.0)
box.lattice = np.array([cell1, cell2, cell3]) box.lattice = np.array([cell1, cell2, cell3]).T
box.lattice_inv = np.linalg.inv(box.lattice) box.lattice_inv = np.linalg.inv(box.lattice)
boxes.append(box) boxes.append(box)
# if first box, start here # if first box, start here
...@@ -2440,7 +2440,7 @@ def vaspTrajecParser(filename, min_boxes=0, max_boxes=1000): ...@@ -2440,7 +2440,7 @@ def vaspTrajecParser(filename, min_boxes=0, max_boxes=1000):
#print(counter, line.split()) #print(counter, line.split())
cell = np.array([cell1, cell2, cell3]) cell = np.array([cell1, cell2, cell3])
rel_coords = np.array([float(ii) for ii in line.split()]) rel_coords = np.array([float(ii) for ii in line.split()])
abs_coords = cell.dot(rel_coords) abs_coords = cell.T.dot(rel_coords)
coordinates.append(abs_coords) coordinates.append(abs_coords)
counter += 1 counter += 1
return boxes return boxes
...@@ -3181,7 +3181,7 @@ def parseVaspFile(fname): ...@@ -3181,7 +3181,7 @@ def parseVaspFile(fname):
for jj in range(ntypat[ii]): for jj in range(ntypat[ii]):
atomType.append(elements[ii]) atomType.append(elements[ii])
# get absolute atom positions # get absolute atom positions
xabs = [np.dot(lattice, xred[ii]) for ii in range(len(xred))] xabs = [np.dot(lattice.T, xred[ii]) for ii in range(len(xred))]
# create the box # create the box
xyzAtoms = [] xyzAtoms = []
for ii in range(len(xabs)): for ii in range(len(xabs)):
...@@ -3295,7 +3295,7 @@ def parseOCEANinputFile(fname): ...@@ -3295,7 +3295,7 @@ def parseOCEANinputFile(fname):
for at in typat: for at in typat:
atoms.append(atoms_name[at-1]) atoms.append(atoms_name[at-1])
xabs = [np.dot(lattice, xred[ii]) for ii in range(len(xred))] xabs = [np.dot(lattice.T, xred[ii]) for ii in range(len(xred))]
xyzAtoms = [] xyzAtoms = []
for ii in range(len(xabs)): for ii in range(len(xabs)):
...@@ -3303,8 +3303,8 @@ def parseOCEANinputFile(fname): ...@@ -3303,8 +3303,8 @@ def parseOCEANinputFile(fname):
box = xyzBox( xyzAtoms ) box = xyzBox( xyzAtoms )
box.lattice = lattice box.lattice = lattice.T
box.lattice_inv = np.linalg.inv(lattice) box.lattice_inv = np.linalg.inv(lattice.T)
box.relAtoms = xred box.relAtoms = xred
return box return box
......
...@@ -381,6 +381,8 @@ class edge_extraction: ...@@ -381,6 +381,8 @@ class edge_extraction:
def removeCorePearsonAv(self,element,edge,range1,range2,weights=[2,1],HFcore_shift=0.0,guess=None,scaling=None,return_background=False): def removeCorePearsonAv(self,element,edge,range1,range2,weights=[2,1],HFcore_shift=0.0,guess=None,scaling=None,return_background=False):
""" """
**removeCorePearsonAv** **removeCorePearsonAv**
guess (list): [position, FWHM, shape, intensity, ax, b, scale ]
""" """
# check that there are averaged signals available # check that there are averaged signals available
if not np.any(self.avsignals): if not np.any(self.avsignals):
......
...@@ -359,6 +359,9 @@ def get_gnuplot_rgb( start=None, end=None, length=None ): ...@@ -359,6 +359,9 @@ def get_gnuplot_rgb( start=None, end=None, length=None ):
for ii in range(len(rgb)): for ii in range(len(rgb)):
print( 'set style line %d lt -1 lc rgb \'#%02x%02x%02x\' lw 1.5'%(ii+1, rgb[ii][0]*255., rgb[ii][1]*255., rgb[ii][2]*255.) ) print( 'set style line %d lt -1 lc rgb \'#%02x%02x%02x\' lw 1.5'%(ii+1, rgb[ii][0]*255., rgb[ii][1]*255., rgb[ii][2]*255.) )
def hex2rgb( hex_val ):
return tuple( int(hex_val.lstrip('#')[i:i+2], 16) for i in (0, 2, 4) )
class maxipix_det: class maxipix_det:
""" """
Class to store some useful values from the detectors used. To be used for arranging the ROIs. Class to store some useful values from the detectors used. To be used for arranging the ROIs.
......
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