def test_validate_formula():
examples = {
'H2O': True,
'Mn(SO4)2(H2O)7': True,
'Mn(SO42(H2O)7': False,
'Z': False
}
for formula, cert in examples.items():
ret = validate_formula(formula)
assert (ret == cert)
def reflectivity(material=None):
message = []
ref_plot = angc_plot = {}
has_data = False
de = '50'
if request.method == 'POST':
formula1 = request.form.get('formula1', 'None')
density1 = request.form.get('density1', '')
angle1 = request.form.get('angle1', '0')
material1 = request.form.get('mats1', 'silicon')
e1 = request.form.get('e1', '1000')
e2 = request.form.get('e2', '50000')
de = request.form.get('de', '50')
mode = request.form.get('mode', 'Linear')
roughness = request.form.get('roughness')
polarization = request.form.get('polarization')
if not xraydb.validate_formula(formula1):
message.append("cannot interpret chemical formula")
try:
density = max(0, float(density1))
except:
message.append('Density must be a positive number.')
if len(message) == 0:
has_data = True
en_array = energy_array(e1, e2, de)
use_log = mode.lower() == 'log'
ref_array = xraydb.mirror_reflectivity(formula1,
0.001 * float(angle1),
en_array,
density,
roughness=float(roughness),
polarization=polarization)
title = "%s, %s mrad" % (formula1, angle1)
ref_plot = make_plot(en_array,
ref_array,
title,
formula1,
yformat='.3f',
ytitle='Reflectivity',
ylog_scale=use_log)
title = "%s Reflectivity, %s mrad" % (formula1, angle1)
ref_plot = make_plot(en_array,
ref_array,
title,
formula1,
yformat='.3f',
ytitle='Reflectivity',
ylog_scale=use_log)
_del, _bet, _ = xraydb.xray_delta_beta(formula1, density, en_array)
ang_crit = 1000 * np.arccos(1 - _del - 1j * _bet).real
title = "%s, Critical Angle" % (formula1)
angc_plot = make_plot(en_array,
ang_crit,
title,
formula1,
ytitle='Critical Angle (mrad)',
ylog_scale=use_log)
else:
request.form = {
'mats1': 'silicon',
'formula1': materials_['silicon'].formula,
'density1': materials_['silicon'].density,
'angle1': 2.5,
'mats2': 'None',
'formula2': '',
'density2': '',
'angle2': 2.5,
'e1': 1000,
'e2': 50000,
'de': de,
'polarization': 's',
'roughness': '0',
'mode': 'Linear'
}
return render_template('reflectivity.html',
message=message,
errors=len(message),
ref_plot=ref_plot,
angc_plot=angc_plot,
has_data=has_data,
matlist=mirror_mat,
de=int(de),
materials_dict=materials_dict)
def atten(material=None,
density=None,
t='1.0',
e1='1000',
e2='51000',
de='50'):
message = []
mu_plot = atten_plot = {}
num = errors = 0
mode = 'Linear'
datalink = None
do_plot = True
if request.method == 'POST':
formula = request.form.get('formula')
matname = request.form.get('matname')
mode = request.form.get('mode')
density = float(request.form.get('density'))
e1 = float(request.form.get('e1'))
e2 = float(request.form.get('e2'))
de = float(request.form.get('de'))
t = float(request.form.get('thickness'))
#input validation
if not xraydb.validate_formula(formula):
message.append("cannot interpret chemical formula")
try:
density = max(0, float(density))
except:
message.append('Density must be a positive number.')
else:
e1 = float(e1)
e2 = float(e2)
de = float(de)
t = float(t)
if material in materials_:
mats = material
formula = materials_['material'].formula
density = materials_['material'].density
elif material is not None and density is not None:
formula = material
density = float(density)
mats = None
else:
do_plot = False
mats = 'silicon'
formula = materials_['silicon'].formula
density = materials_['silicon'].density
request.form = {
'mats': mats,
'formula': formula,
'density': density,
'e1': e1,
'e2': e2,
'de': de,
'thickness': t,
'mode': 'Linear'
}
if do_plot and formula is not None:
# make plot
en_array = energy_array(e1, e2, de)
num = en_array.size
mu_array = xraydb.material_mu(formula,
en_array,
density=float(density))
trans = np.exp(-0.1 * t * mu_array)
atten = 1 - trans
use_log = mode.lower() == 'log'
mu_plot = make_plot(en_array,
10 / mu_array,
material,
formula,
ylog_scale=use_log,
ytitle='1/e length (mm)')
atten_plot = make_plot(en_array,
trans,
material,
"%.3f mm %s" % (t, formula),
ylog_scale=use_log,
y2=atten,
ytitle='transmitted/attenuated fraction',
y1label='transmitted',
y2label='attenuated')
return render_template('attenuation.html',
message=message,
errors=len(message),
datalink=datalink,
mu_plot=mu_plot,
de=int(de),
atten_plot=atten_plot,
matlist=matlist,
materials_dict=materials_dict) # , input=input)
def validate_input(formula,
density,
step,
energy1='1000',
energy2='50000',
mode='Log',
material=None,
angle='0.001',
roughness='0.0',
page='formula'):
output = {}
message = []
message.append('Error(s): ')
df = ef = ef2 = sf = af = rf = 0
isLog = True
if not formula:
message.append('Formula is a required field.')
elif not material:
#verify formula using function
if not xraydb.validate_formula(formula):
message.append('Unable to compute formula.')
if density:
try:
df = float(density)
if df <= 0:
message.append('Density must be a positive number.')
except:
message.append('Density must be a positive number.')
else:
message.append('Density is a required field.')
if energy1:
ef = float(energy1)
else:
ef = 1000.0
if energy2:
ef2 = float(energy2)
else:
ef2 = 50000.0
sf = float(step)
if ef > ef2:
message.append('Energy1 must be less than Energy2.')
isLog = True if mode == 'Log' else False
if page == 'reflectivity':
if angle:
af = float(angle)
else:
af = 0.001
if roughness:
rf = float(roughness)
else:
rf = 0.0
if len(message) == 1:
message[0] = 'Input is valid'
output['message'] = message
if message[0] == 'Input is valid':
output['df'] = df
output['ef'] = ef
output['ef2'] = ef2
output['sf'] = sf
output['isLog'] = isLog
output['af'] = af
output['rf'] = rf
#print(message)
return output
def atten(material=None):
message = []
energies = []
mu_plot = atten_plot = {}
num = errors = 0
mode = 'Linear'
datalink = None
if request.method == 'POST':
formula = request.form.get('formula')
matname = request.form.get('matname')
density = request.form.get('density')
energy1 = request.form.get('energy1')
energy2 = request.form.get('energy2')
estep = request.form.get('step')
mode = request.form.get('mode')
thickness = request.form.get('thickness')
#input validation
if not xraydb.validate_formula(formula):
message.append("cannot interpret chemical formula")
try:
density = max(0, float(density))
except:
message.append('Density must be a positive number.')
if len(message) == 0:
use_log = mode.lower() == 'log'
# make plot
en_array = np.arange(float(energy1), float(energy2)+float(estep), float(estep))
num = en_array.size
mu_array = xraydb.material_mu(formula, en_array, density=float(density))
t = float(thickness)
trans = np.exp(-0.1*t*mu_array)
atten = 1 - trans
mu_plot = make_plot(en_array, 10/mu_array, material, formula,
ylog_scale=use_log, ytitle='1/e length (mm)')
atten_plot = make_plot(en_array, trans,
material, "%.3f mm %s" % (t, formula),
ylog_scale=use_log,
y2=atten,
ytitle='transmitted/attenuated fraction',
y1label='transmitted',
y2label='attenuated')
else:
request.form = {'mats': 'silicon',
'formula': materials_['silicon'].formula,
'density': materials_['silicon'].density,
'energy1': 1000,
'energy2': 51000,
'step': "50",
'thickness': 1.00,
'mode': 'Linear'}
return render_template('attenuation.html', message=message, errors=len(message),
datalink=datalink, mu_plot=mu_plot,
atten_plot=atten_plot, matlist=matlist,
materials_dict=materials_dict, input=input)