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Windows Fixes and searching for cctbx in home directory
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@bcolsen
bcolsen committed Jun 21, 2017
1 parent 28a71a5 commit 5f2dc1f
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Showing 2 changed files with 116 additions and 90 deletions.
5 changes: 4 additions & 1 deletion diff_win.spec
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,10 @@ block_cipher = None
a = Analysis(['diffraction_ring_profiler.py'],
pathex=['C:\\Users\\owner\\diff-ring'],
binaries=[],
datas=[('icons', 'icons')],
datas=[('icons', 'icons'),
('examples', 'examples'),
('iotbx_cif.py', '.'),
('README.md', '.')],
hiddenimports=[],
hookspath=[],
runtime_hooks=[],
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201 changes: 112 additions & 89 deletions profile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -962,118 +962,141 @@ def OnSimOpen(self,e):
# application. In theory, you could create one earlier, store it in
# your frame object and change it when it was called to reflect
# current parameters / values
dlg = wx.FileDialog(self, "Choose a CIF crystal file",
self.dirname, "", "CIF|*.cif;*.CIF|All Files|*.*", wx.FD_OPEN)
if dlg.ShowModal() == wx.ID_OK:

filename=dlg.GetFilename()
self.dirname=dlg.GetDirectory()

print(self.dirname)

#print(count, centers, circle)

name, ext = os.path.splitext(filename)

cctbx_python_path = None

di_max = 1.4
d_min = str(1/1.4)

cif_name = os.path.join(self.dirname, filename)

cctbx_python_path = '/usr/local/cctbx-dev-1065/build/bin/cctbx.python'

def voigt(x,amp,pos,fwhm,shape):
"""\
voigt profile
V(x,sig,gam) = Re(w(z))/(sig*sqrt(2*pi))
z = (x+i*gam)/(sig*sqrt(2))
"""

tmp = 1/special.wofz(np.zeros((len(x))) \
+1j*np.sqrt(np.log(2.0))*shape).real
tmp = tmp*amp* \
special.wofz(2*np.sqrt(np.log(2.0))*(x-pos)/fwhm+1j* \
np.sqrt(np.log(2.0))*shape).real
return tmp
# Look for cctbx.python
home = os.path.expanduser('~')
#print(os.listdir(home))
for f_name in os.listdir(home):
if f_name.startswith('cctbx'):
cctbx_python_path = os.path.join(home,f_name,'build','bin','cctbx.python')

if cctbx_python_path == None:
error_cctbx = 'Could not find cctbx.\nPlease download cctbx: http://cci.lbl.gov/cctbx_build/ \nand extract it to: ' + str(home)
print(error_cctbx)
error_int_dlg = Error(self, -1, 'Error', error_cctbx)
error_int_dlg.Show(True)
error_int_dlg.Centre()
else:
dlg = wx.FileDialog(self, "Choose a CIF crystal file",
self.dirname, "", "CIF|*.cif;*.CIF|All Files|*.*", wx.FD_OPEN)
if dlg.ShowModal() == wx.ID_OK:

filename=dlg.GetFilename()
self.dirname=dlg.GetDirectory()

print(self.dirname)

#print(count, centers, circle)

name, ext = os.path.splitext(filename)

di_max = 1.4
d_min = str(1/1.4)

cctbx_script_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'iotbx_cif.py'))
cif_name = os.path.join(self.dirname, filename)

def voigt(x,amp,pos,fwhm,shape):
"""\
voigt profile
print(cctbx_python_path, cctbx_script_path)
V(x,sig,gam) = Re(w(z))/(sig*sqrt(2*pi))
z = (x+i*gam)/(sig*sqrt(2))
"""

sf_output, sf_error = subprocess.Popen([cctbx_python_path, cctbx_script_path, cif_name, d_min, 'sf'], stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
print(sf_output)
tmp = 1/special.wofz(np.zeros((len(x))) \
+1j*np.sqrt(np.log(2.0))*shape).real
tmp = tmp*amp* \
special.wofz(2*np.sqrt(np.log(2.0))*(x-pos)/fwhm+1j* \
np.sqrt(np.log(2.0))*shape).real
return tmp

ds_output, sf_error = subprocess.Popen([cctbx_python_path, cctbx_script_path, cif_name, d_min, 'ds'], stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
print(ds_output)
cctbx_script_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'iotbx_cif.py'))

mt_output, sf_error = subprocess.Popen([cctbx_python_path, cctbx_script_path, cif_name, d_min, 'mt'], stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
print(mt_output)
print(cctbx_python_path, cctbx_script_path)

shell_args = [cctbx_python_path, cctbx_script_path, cif_name, d_min, 'sf']
pro_args = dict(args = shell_args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
if os.name == 'nt':
pro_args['shell'] = True

shell_args[-1] = 'sf'
sf_output, sf_error = subprocess.Popen(**pro_args).communicate()
print(sf_output)

shell_args[-1] = 'ds'
ds_output, sf_error = subprocess.Popen(**pro_args).communicate()
print(ds_output)

shell_args[-1] = 'mt'
mt_output, sf_error = subprocess.Popen(**pro_args).communicate()
print(mt_output)

sf_data = genfromtxt(BytesIO(sf_output), dtype=None, names=('h','k','l','sf'))
sf_data = genfromtxt(BytesIO(sf_output), dtype=None, names=('h','k','l','sf'))

#print sf_data.shape
sf= sf_data['sf']
print(sf)
#print sf_data.shape
sf= sf_data['sf']
print(sf)

ds_data = genfromtxt(BytesIO(ds_output), dtype=None, names=('h','k','l','ds'))
ds_data = genfromtxt(BytesIO(ds_output), dtype=None, names=('h','k','l','ds'))

#print ds_data.shape
ds= ds_data['ds']
print(ds)
#print ds_data.shape
ds= ds_data['ds']
print(ds)

mt_data = genfromtxt(BytesIO(mt_output), dtype=None, names=('h','k','l','mt'))
mt_data = genfromtxt(BytesIO(mt_output), dtype=None, names=('h','k','l','mt'))

#print ds_data.shape
mt= mt_data['mt']
print(mt)
#print ds_data.shape
mt= mt_data['mt']
print(mt)


hkl_list = []
for h,k,l in zip(ds_data['h'],ds_data['k'],ds_data['l']):
hkl_list += [''.join([str(h.translate(None,b' (),'),"utf-8"), str(k.translate(None,b' (),'),"utf-8"), str(l.translate(None,b' (),'),"utf-8")])]

print(hkl_list)
hkl_list = []
for h,k,l in zip(ds_data['h'],ds_data['k'],ds_data['l']):
hkl_list += [''.join([str(h.translate(None,b' (),'),"utf-8"), str(k.translate(None,b' (),'),"utf-8"), str(l.translate(None,b' (),'),"utf-8")])]
print(hkl_list)

sol2 = (0.5/ds)**2
sol2 = (0.5/ds)**2

sfc = (sf)/sol2
sfc = (sf)/sol2

sfc2 = (sf)/((1/ds)**(2+.5))
sfc2 = (sf)/((1/ds)**(2+.5))


int1 = sfc*mt
int2 = sfc2*mt
int1 = sfc*mt
int2 = sfc2*mt

int2n = int2/int2.max()
int1n = int1/int1.max()
int2n = int2/int2.max()
int1n = int1/int1.max()

## Broden
x = np.linspace(0,di_max,1000)
di =1/ds
vois =[]
for i,d in zip(int2n,di):
vois += [voigt(x,i,d,0.025,1)]
## Broden
x = np.linspace(0,di_max,1000)
di =1/ds
vois =[]
for i,d in zip(int2n,di):
vois += [voigt(x,i,d,0.025,1)]

brd = np.array(vois).sum(axis=0)
brd = np.array(vois).sum(axis=0)

dtypes = [('inv_d',float),('intensity',float),('index','<U4')]
sim_open = np.array(list(zip(di,int2n,hkl_list)), dtypes)
sim_open.sort(order='inv_d')
print(sim_open,sim_open.shape,len(sim_open.shape))
self.simulations += [Simulation(name, sim_open[['inv_d','intensity']], sim_open['index'])]

self.plot_sim = 1
self.prosim = 1
self.prosim_int = brd
self.prosim_inv_d = x

self.axes.cla()
self.plot(2,'b')

self.axes.figure.canvas.draw()

dlg.Destroy()
dtypes = [('inv_d',float),('intensity',float),('index','<U4')]
sim_open = np.array(list(zip(di,int2n,hkl_list)), dtypes)
sim_open.sort(order='inv_d')
print(sim_open,sim_open.shape,len(sim_open.shape))
self.simulations += [Simulation(name, sim_open[['inv_d','intensity']], sim_open['index'])]
self.plot_sim = 1
self.prosim = 1
self.prosim_int = brd
self.prosim_inv_d = x
self.axes.cla()
self.plot(2,'b')
self.axes.figure.canvas.draw()
dlg.Destroy()

def OnSim2Open(self,e):
# In this case, the dialog is created within the method because
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