Commit adab0a7f authored by christoph's avatar christoph
Browse files

small bug fixes

parent 5a39cd57
......@@ -1975,7 +1975,7 @@ class roi_finder:
ax1.legend(['Row No. %02d / %02d' %(1, rw_data[roi_keys[0]].shape[1])],
frameon=False, loc=1, fontsize='x-small')
# 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-')
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 )
......
......@@ -2371,11 +2371,11 @@ def vaspBoxParser(filename):
for ind in range(num_atoms[zz]):
# print(ind, kind, cou)
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 ))
cou += 1
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)
return box
......@@ -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))
coorcou += 1
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)
boxes.append(box)
# if first box, start here
......@@ -2440,7 +2440,7 @@ def vaspTrajecParser(filename, min_boxes=0, max_boxes=1000):
#print(counter, line.split())
cell = np.array([cell1, cell2, cell3])
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)
counter += 1
return boxes
......@@ -3181,7 +3181,7 @@ def parseVaspFile(fname):
for jj in range(ntypat[ii]):
atomType.append(elements[ii])
# 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
xyzAtoms = []
for ii in range(len(xabs)):
......@@ -3295,7 +3295,7 @@ def parseOCEANinputFile(fname):
for at in typat:
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 = []
for ii in range(len(xabs)):
......@@ -3303,8 +3303,8 @@ def parseOCEANinputFile(fname):
box = xyzBox( xyzAtoms )
box.lattice = lattice
box.lattice_inv = np.linalg.inv(lattice)
box.lattice = lattice.T
box.lattice_inv = np.linalg.inv(lattice.T)
box.relAtoms = xred
return box
......
......@@ -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):
"""
**removeCorePearsonAv**
guess (list): [position, FWHM, shape, intensity, ax, b, scale ]
"""
# check that there are averaged signals available
if not np.any(self.avsignals):
......
......@@ -359,6 +359,9 @@ def get_gnuplot_rgb( start=None, end=None, length=None ):
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.) )
def hex2rgb( hex_val ):
return tuple( int(hex_val.lstrip('#')[i:i+2], 16) for i in (0, 2, 4) )
class maxipix_det:
"""
Class to store some useful values from the detectors used. To be used for arranging the ROIs.
......
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