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language: python
python:
- 3.6
- 3.7
- 3.8
# Build only tagged commits
if: tag IS present
before_install:
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
- bash miniconda.sh -b -p $HOME/miniconda
- export PATH="$HOME/miniconda/bin:$PATH"
- conda config --append channels conda-forge
- conda config --set always_yes yes
- conda config --set anaconda_upload no
install:
- conda update -q conda
- conda install -q python=$TRAVIS_PYTHON_VERSION conda-build anaconda-client
script:
- conda build conda-recipe
deploy:
provider: script
script: anaconda -t $ANACONDA_TOKEN upload $HOME/miniconda/conda-bld/**/pyzebra-*.tar.bz2
on:
branch: master
tags: true
notifications:
email: false

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GNU GENERAL PUBLIC LICENSE
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How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
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To do so, attach the following notices to the program. It is safest
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streamvis
Copyright (C) 2018 Ivan Usov
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
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You should have received a copy of the GNU General Public License
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Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
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streamvis Copyright (C) 2018 Ivan Usov
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<http://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<http://www.gnu.org/philosophy/why-not-lgpl.html>.

2
conda-recipe/build.sh Normal file
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@ -0,0 +1,2 @@
#!/bin/bash
$PYTHON setup.py install --single-version-externally-managed --record=record.txt

34
conda-recipe/meta.yaml Normal file
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@ -0,0 +1,34 @@
{% set data = load_setup_py_data() %}
package:
name: pyzebra
version: {{ data['version'] }}
source:
path: ..
build:
number: 0
entry_points:
- pyzebra = pyzebra.cli:main
requirements:
build:
- python
- setuptools
run:
- python
- numpy
- scipy
- h5py
- bokeh
- numba
- lmfit
- uncertainties
about:
home: https://github.com/paulscherrerinstitute/pyzebra
summary: {{ data['description'] }}
license: GNU GPLv3
license_file: LICENSE

46
pyzebra/app/panel_hdf_viewer.py
View File

@ -83,6 +83,12 @@ def create():
image_glyph.color_mapper.low = im_min
image_glyph.color_mapper.high = im_max
magnetic_field_spinner.value = det_data["magnetic_field"][index]
temperature_spinner.value = det_data["temperature"][index]
gamma, nu = calculate_pol(det_data, index)
image_source.data.update(gamma=[gamma], nu=[nu])
def update_overview_plot():
h5_data = det_data["data"]
n_im, n_y, n_x = h5_data.shape
@ -153,6 +159,8 @@ def create():
h=[np.zeros((1, 1))],
k=[np.zeros((1, 1))],
l=[np.zeros((1, 1))],
gamma=[np.zeros((1, 1))],
nu=[np.zeros((1, 1))],
x=[0],
y=[0],
dw=[IMAGE_W],
@ -163,10 +171,14 @@ def create():
h_glyph = Image(image="h", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
k_glyph = Image(image="k", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
l_glyph = Image(image="l", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
gamma_glyph = Image(image="gamma", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
nu_glyph = Image(image="nu", x="x", y="y", dw="dw", dh="dh", global_alpha=0)
plot.add_glyph(image_source, h_glyph)
plot.add_glyph(image_source, k_glyph)
plot.add_glyph(image_source, l_glyph)
plot.add_glyph(image_source, gamma_glyph)
plot.add_glyph(image_source, nu_glyph)
image_glyph = Image(image="image", x="x", y="y", dw="dw", dh="dh")
plot.add_glyph(image_source, image_glyph, name="image_glyph")
@ -207,7 +219,16 @@ def create():
proj_h.add_glyph(proj_h_line_source, Line(x="x", y="y", line_color="steelblue"))
# add tools
hovertool = HoverTool(tooltips=[("intensity", "@image"), ("h", "@h"), ("k", "@k"), ("l", "@l")])
hovertool = HoverTool(
tooltips=[
("intensity", "@image"),
("gamma", "@gamma"),
("nu", "@nu"),
("h", "@h"),
("k", "@k"),
("l", "@l"),
]
)
box_edit_source = ColumnDataSource(dict(x=[], y=[], width=[], height=[]))
box_edit_glyph = Rect(
@ -438,12 +459,18 @@ def create():
selection_button = Button(label="Add selection")
selection_button.on_click(selection_button_callback)
magnetic_field_spinner = Spinner(
title="Magnetic field:", format="0.00", width=145, disabled=True
)
temperature_spinner = Spinner(title="Temperature:", format="0.00", width=145, disabled=True)
# Final layout
layout_image = column(
gridplot([[proj_v, None], [plot, proj_h]], merge_tools=False), row(index_spinner)
)
colormap_layout = column(colormap, auto_toggle, display_max_spinner, display_min_spinner)
hkl_layout = column(radio_button_group, hkl_button)
params_layout = row(magnetic_field_spinner, temperature_spinner)
layout_overview = column(
gridplot(
@ -461,7 +488,7 @@ def create():
layout_overview,
row(frame_button_group, selection_button, selection_list),
),
column(roi_avg_plot, layout_image, row(colormap_layout, hkl_layout)),
column(roi_avg_plot, layout_image, row(colormap_layout, column(params_layout, hkl_layout))),
)
return Panel(child=tab_layout, title="hdf viewer")
@ -495,3 +522,18 @@ def calculate_hkl(det_data, index, setup_type="nb_bi"):
)
return h, k, l
def calculate_pol(det_data, index):
gamma = np.empty(shape=(IMAGE_H, IMAGE_W))
nu = np.empty(shape=(IMAGE_H, IMAGE_W))
ddist = det_data["ddist"]
gammad = det_data["pol_angle"][index]
nud = det_data["tlt_angle"]
for xi in np.arange(IMAGE_W):
for yi in np.arange(IMAGE_H):
gamma[yi, xi], nu[yi, xi] = pyzebra.det2pol(ddist, gammad, nud, xi, yi)
return gamma, nu

2
pyzebra/h5.py
View File

@ -60,6 +60,8 @@ def read_detector_data(filepath):
det_data["chi_angle"] = h5f["/entry1/sample/chi"][:] # ch
det_data["phi_angle"] = h5f["/entry1/sample/phi"][:] # ph
det_data["UB"] = h5f["/entry1/sample/UB"][:].reshape(3, 3)
det_data["magnetic_field"] = h5f["/entry1/sample/magnetic_field"][:]
det_data["temperature"] = h5f["/entry1/sample/temperature"][:]
return det_data

68
pyzebra/xtal.py
View File

@ -1,6 +1,7 @@
import math
import numpy as np
from numba import njit
from scipy.optimize import curve_fit
import pyzebra
@ -10,6 +11,7 @@ try:
except ImportError:
print("matplotlib is not available")
pi_r = 180 / np.pi
def z4frgn(wave, ga, nu):
@ -21,19 +23,17 @@ def z4frgn(wave, ga, nu):
Returns:
Z4
"""
sin = np.sin
cos = np.cos
pir = 180 / np.pi
gar = ga / pir
nur = nu / pir
ga_r = ga / pi_r
nu_r = nu / pi_r
z4 = [0.0, 0.0, 0.0]
z4[0] = (sin(gar) * cos(nur)) / wave
z4[1] = (cos(gar) * cos(nur) - 1.0) / wave
z4[2] = (sin(nur)) / wave
z4[0] = (np.sin(ga_r) * np.cos(nu_r)) / wave
z4[1] = (np.cos(ga_r) * np.cos(nu_r) - 1.0) / wave
z4[2] = (np.sin(nu_r)) / wave
return z4
@njit(cache=True)
def phimat(phi):
"""BUSING AND LEVY CONVENTION ROTATION MATRIX FOR PHI OR OMEGA
@ -43,14 +43,11 @@ def phimat(phi):
Returns:
DUM
"""
sin = np.sin
cos = np.cos
pir = 180 / np.pi
phr = phi / pir
ph_r = phi / pi_r
dum = np.zeros(9).reshape(3, 3)
dum[0, 0] = cos(phr)
dum[0, 1] = sin(phr)
dum[0, 0] = np.cos(ph_r)
dum[0, 1] = np.sin(ph_r)
dum[1, 0] = -dum[0, 1]
dum[1, 1] = dum[0, 0]
dum[2, 2] = 1
@ -67,7 +64,6 @@ def z1frnb(wave, ga, nu, om):
Returns:
Z1
"""
z4 = z4frgn(wave, ga, nu)
dum = phimat(phi=om)
dumt = np.transpose(dum)
@ -76,6 +72,7 @@ def z1frnb(wave, ga, nu, om):
return z3
@njit(cache=True)
def chimat(chi):
"""BUSING AND LEVY CONVENTION ROTATION MATRIX FOR CHI
@ -85,14 +82,11 @@ def chimat(chi):
Returns:
DUM
"""
sin = np.sin
cos = np.cos
pir = 180 / np.pi
chr = chi / pir
ch_r = chi / pi_r
dum = np.zeros(9).reshape(3, 3)
dum[0, 0] = cos(chr)
dum[0, 2] = sin(chr)
dum[0, 0] = np.cos(ch_r)
dum[0, 2] = np.sin(ch_r)
dum[1, 1] = 1
dum[2, 0] = -dum[0, 2]
dum[2, 2] = dum[0, 0]
@ -100,6 +94,7 @@ def chimat(chi):
return dum
@njit(cache=True)
def z1frz3(z3, chi, phi):
"""CALCULATE Z1 = [PHI]T.[CHI]T.Z3
@ -109,7 +104,6 @@ def z1frz3(z3, chi, phi):
Returns:
Z1
"""
dum1 = chimat(chi)
dum2 = np.transpose(dum1)
z2 = dum2.dot(z3)
@ -136,6 +130,7 @@ def z1frmd(wave, ga, om, chi, phi, nu):
return z1
@njit(cache=True)
def det2pol(ddist, gammad, nud, x, y):
"""CONVERTS FROM DETECTOR COORDINATES TO POLAR COORDINATES
@ -157,10 +152,9 @@ def det2pol(ddist, gammad, nud, x, y):
b = ddist * np.cos(yobs / ddist)
z = ddist * np.sin(yobs / ddist)
d = np.sqrt(a * a + b * b)
pir = 180 / np.pi
gamma = gammad + np.arctan2(a, b) * pir
nu = nud + np.arctan2(z, d) * pir
gamma = gammad + np.arctan2(a, b) * pi_r
nu = nud + np.arctan2(z, d) * pi_r
return gamma, nu
@ -174,14 +168,12 @@ def eqchph(z1):
Returns:
chi, phi
"""
pir = 180 / np.pi
if z1[0] != 0 or z1[1] != 0:
ph = np.arctan2(z1[1], z1[0])
ph = ph * pir
ph = ph * pi_r
d = np.sqrt(z1[0] * z1[0] + z1[1] * z1[1])
ch = np.arctan2(z1[2], d)
ch = ch * pir
ch = ch * pi_r
else:
ph = 0
ch = 90
@ -203,8 +195,6 @@ def dandth(wave, z1):
Returns:
ds, th
"""
pir = 180 / np.pi
ierr = 0
dstar = np.sqrt(z1[0] * z1[0] + z1[1] * z1[1] + z1[2] * z1[2])
@ -212,7 +202,7 @@ def dandth(wave, z1):
ds = 1 / dstar
sint = wave * dstar / 2
if np.abs(sint) <= 1:
th = np.arcsin(sint) * pir
th = np.arcsin(sint) * pi_r
else:
ierr = 2
th = 0
@ -262,8 +252,6 @@ def fixdnu(wave, z1, ch2, ph2, nu):
Returns:
tth, om, ch, ph
"""
pir = 180 / np.pi
tth, om, ch, ph, ierr = angs4c(wave, z1, ch2, ph2)
theta = om
if ierr != 0:
@ -272,13 +260,13 @@ def fixdnu(wave, z1, ch2, ph2, nu):
ga = 0
om = 0
else:
if np.abs(np.cos(nu / pir)) > 0.0001:
cosga = np.cos(tth / pir) / np.cos(nu / pir)
if np.abs(np.cos(nu / pi_r)) > 0.0001:
cosga = np.cos(tth / pi_r) / np.cos(nu / pi_r)
if np.abs(cosga) <= 1:
ga = np.arccos(cosga) * pir
ga = np.arccos(cosga) * pi_r
z4 = z4frgn(wave, ga, nu)
om = np.arctan2(-z4[1], z4[0]) * pir
ch2 = np.arcsin(z4[2] * wave / (2 * np.sin(theta / pir))) * pir
om = np.arctan2(-z4[1], z4[0]) * pi_r
ch2 = np.arcsin(z4[2] * wave / (2 * np.sin(theta / pi_r))) * pi_r
ch = ch - ch2
ch = ch - 360 * np.trunc((np.sign(ch) * 180 + ch) / 360)
else:
@ -317,8 +305,6 @@ def angtohkl(wave, ddist, gammad, om, ch, ph, nud, x, y):
Returns:
"""
pir = 180 / np.pi
# define ub matrix if testing angtohkl(wave=1.18,ddist=616,gammad=48.66,om=-22.80,ch=0,ph=0,nud=0,x=128,y=64) against f90:
# ub = np.array([-0.0178803,-0.0749231,0.0282804,-0.0070082,-0.0368001,-0.0577467,0.1609116,-0.0099281,0.0006274]).reshape(3,3)
ub = np.array(