13 Commits
0.7.3 ... 0.7.6

Author SHA1 Message Date
90552cee2c Updating for version 0.7.6 2023-08-02 15:17:06 +02:00
6164be16f0 fix y axis label in projection plot 2023-08-02 14:41:49 +02:00
07f03a2a04 Add .gitlab-ci.yml 2023-07-27 15:17:31 +02:00
f89267b5ec Updating for version 0.7.5 2023-07-02 22:59:36 +02:00
8e6cef32b5 Use libmamba solver 2023-07-02 22:59:11 +02:00
e318055304 Replace depricated dtype aliases
For numpy>=1.20
2023-07-02 22:32:43 +02:00
015eb095a4 Prepare for transition to bokeh/3
* Rename plot_height -> height
* Rename plot_width -> width
* Replace on_click callbacks of RadioGroup and CheckboxGroup
2023-06-20 15:54:47 +02:00
d145f9107d Drop python/3.7 support 2023-06-20 14:52:26 +02:00
d1a0ba6fec Fix for gamma with the new data format
Fix #57
2023-06-06 13:53:10 +02:00
2e2677d856 Set chi=180, phi=0 for nb geometry 2023-06-01 16:18:50 +02:00
a165167902 Updating for version 0.7.4 2023-05-25 13:51:29 +02:00
0b88ab0c7f Use scan["nu"] as a scalar
Fix #53
2023-05-23 08:56:18 +02:00
59d392c9ec Update to a new data format in ccl/dat files 2023-05-16 11:26:08 +02:00
15 changed files with 135 additions and 88 deletions

View File

@ -14,8 +14,9 @@ jobs:
- name: Prepare
run: |
$CONDA/bin/conda install --quiet --yes conda-build anaconda-client
$CONDA/bin/conda install --quiet --yes conda-build anaconda-client conda-libmamba-solver
$CONDA/bin/conda config --append channels conda-forge
$CONDA/bin/conda config --set solver libmamba
$CONDA/bin/conda config --set anaconda_upload yes
- name: Build and upload

24
.gitlab-ci.yml Normal file
View File

@ -0,0 +1,24 @@
stages:
- deploy-test
- deploy-prod
deploy-test:
stage: deploy-test
rules:
- if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
script:
- cd /opt/pyzebra
- git pull origin master --tags
- sudo systemctl restart pyzebra-test.service
deploy-prod:
stage: deploy-prod
rules:
- if: $CI_COMMIT_TAG && $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
when: delayed
start_in: 10 minutes
script:
- source /opt/miniconda3/etc/profile.d/conda.sh
- conda activate prod
- conda update pyzebra -y
- sudo systemctl restart pyzebra.service

View File

@ -15,10 +15,10 @@ build:
requirements:
build:
- python >=3.7
- python >=3.8
- setuptools
run:
- python >=3.7
- python >=3.8
- numpy
- scipy
- h5py

View File

@ -6,4 +6,4 @@ from pyzebra.sxtal_refgen import *
from pyzebra.utils import *
from pyzebra.xtal import *
__version__ = "0.7.3"
__version__ = "0.7.6"

View File

@ -243,8 +243,8 @@ def create():
plot = figure(
x_axis_label="Scan motor",
y_axis_label="Counts",
plot_height=470,
plot_width=700,
height=470,
width=700,
tools="pan,wheel_zoom,reset",
)

View File

@ -112,8 +112,8 @@ def create():
plot = figure(
x_axis_label="Scan motor",
y_axis_label="Counts",
plot_height=470,
plot_width=700,
height=470,
width=700,
tools="pan,wheel_zoom,reset",
)

View File

@ -604,7 +604,7 @@ def create():
plot_file = Button(label="Plot selected file(s)", button_type="primary", width=200)
plot_file.on_click(plot_file_callback)
plot = figure(plot_height=550, plot_width=550 + 32, tools="pan,wheel_zoom,reset")
plot = figure(height=550, width=550 + 32, tools="pan,wheel_zoom,reset")
plot.toolbar.logo = None
plot.xaxis.visible = False

View File

@ -301,8 +301,8 @@ def create():
x_range=det_x_range,
y_range=frame_range,
extra_y_ranges={"scanning_motor": scanning_motor_range},
plot_height=540,
plot_width=IMAGE_PLOT_W - 3,
height=540,
width=IMAGE_PLOT_W - 3,
tools="pan,box_zoom,wheel_zoom,reset",
active_scroll="wheel_zoom",
)
@ -325,8 +325,8 @@ def create():
x_range=det_y_range,
y_range=frame_range,
extra_y_ranges={"scanning_motor": scanning_motor_range},
plot_height=540,
plot_width=IMAGE_PLOT_H + 22,
height=540,
width=IMAGE_PLOT_H + 22,
tools="pan,box_zoom,wheel_zoom,reset",
active_scroll="wheel_zoom",
)
@ -352,8 +352,8 @@ def create():
colormap_select.on_change("value", colormap_select_callback)
colormap_select.value = "Plasma256"
def proj_auto_checkbox_callback(state):
if state:
def proj_auto_checkbox_callback(_attr, _old, new):
if 0 in new:
proj_display_min_spinner.disabled = True
proj_display_max_spinner.disabled = True
else:
@ -365,7 +365,7 @@ def create():
proj_auto_checkbox = CheckboxGroup(
labels=["Projections Intensity Range"], active=[0], width=145, margin=[10, 5, 0, 5]
)
proj_auto_checkbox.on_click(proj_auto_checkbox_callback)
proj_auto_checkbox.on_change("active", proj_auto_checkbox_callback)
def proj_display_max_spinner_callback(_attr, _old, new):
color_mapper_proj.high = new
@ -411,8 +411,8 @@ def create():
param_plot = figure(
x_axis_label="Parameter",
y_axis_label="Fit parameter",
plot_height=400,
plot_width=700,
height=400,
width=700,
tools="pan,wheel_zoom,reset",
)

View File

@ -356,8 +356,8 @@ def create():
gamma_c = gamma[det_c_y, det_c_x]
nu_c = nu[det_c_y, det_c_x]
omega_c = omega[det_c_y, det_c_x]
chi_c = None
phi_c = None
chi_c = scan["chi"][index]
phi_c = scan["phi"][index]
else: # zebra_mode == "bi"
wave = scan["wave"]
@ -406,7 +406,7 @@ def create():
frame_range.bounds = (0, n_im)
scan_motor = scan["scan_motor"]
proj_y_plot.axis[1].axis_label = f"Scanning motor, {scan_motor}"
proj_y_plot.yaxis.axis_label = f"Scanning motor, {scan_motor}"
var = scan[scan_motor]
var_start = var[0]
@ -458,8 +458,8 @@ def create():
y_range=Range1d(0, IMAGE_H, bounds=(0, IMAGE_H)),
x_axis_location="above",
y_axis_location="right",
plot_height=IMAGE_PLOT_H,
plot_width=IMAGE_PLOT_W,
height=IMAGE_PLOT_H,
width=IMAGE_PLOT_W,
toolbar_location="left",
tools="pan,box_zoom,wheel_zoom,reset",
active_scroll="wheel_zoom",
@ -509,8 +509,8 @@ def create():
proj_v = figure(
x_range=plot.x_range,
y_axis_location="right",
plot_height=150,
plot_width=IMAGE_PLOT_W,
height=150,
width=IMAGE_PLOT_W,
tools="",
toolbar_location=None,
)
@ -524,8 +524,8 @@ def create():
proj_h = figure(
x_axis_location="above",
y_range=plot.y_range,
plot_height=IMAGE_PLOT_H,
plot_width=150,
height=IMAGE_PLOT_H,
width=150,
tools="",
toolbar_location=None,
)
@ -589,8 +589,8 @@ def create():
y_range=frame_range,
extra_x_ranges={"gamma": gamma_range},
extra_y_ranges={"scanning_motor": scanning_motor_range},
plot_height=540,
plot_width=IMAGE_PLOT_W - 3,
height=540,
width=IMAGE_PLOT_W - 3,
tools="pan,box_zoom,wheel_zoom,reset",
active_scroll="wheel_zoom",
)
@ -617,8 +617,8 @@ def create():
y_range=frame_range,
extra_x_ranges={"nu": nu_range},
extra_y_ranges={"scanning_motor": scanning_motor_range},
plot_height=540,
plot_width=IMAGE_PLOT_H + 22,
height=540,
width=IMAGE_PLOT_H + 22,
tools="pan,box_zoom,wheel_zoom,reset",
active_scroll="wheel_zoom",
)
@ -636,7 +636,7 @@ def create():
proj_y_image = proj_y_plot.image(source=proj_y_image_source, color_mapper=lin_color_mapper_proj)
# ROI slice plot
roi_avg_plot = figure(plot_height=150, plot_width=IMAGE_PLOT_W, tools="", toolbar_location=None)
roi_avg_plot = figure(height=150, width=IMAGE_PLOT_W, tools="", toolbar_location=None)
roi_avg_plot_line_source = ColumnDataSource(dict(x=[], y=[]))
roi_avg_plot.line(source=roi_avg_plot_line_source, line_color="steelblue")
@ -655,8 +655,8 @@ def create():
colormap_select.on_change("value", colormap_select_callback)
colormap_select.value = "Plasma256"
def colormap_scale_rg_callback(selection):
if selection == 0: # Linear
def colormap_scale_rg_callback(_attr, _old, new):
if new == 0: # Linear
plot_image.glyph.color_mapper = lin_color_mapper
proj_x_image.glyph.color_mapper = lin_color_mapper_proj
proj_y_image.glyph.color_mapper = lin_color_mapper_proj
@ -675,10 +675,10 @@ def create():
colormap_scale_rg.active = 0
colormap_scale_rg = RadioGroup(labels=["Linear", "Logarithmic"], active=0, width=100)
colormap_scale_rg.on_click(colormap_scale_rg_callback)
colormap_scale_rg.on_change("active", colormap_scale_rg_callback)
def main_auto_checkbox_callback(state):
if state:
def main_auto_checkbox_callback(_attr, _old, new):
if 0 in new:
display_min_spinner.disabled = True
display_max_spinner.disabled = True
else:
@ -690,7 +690,7 @@ def create():
main_auto_checkbox = CheckboxGroup(
labels=["Frame Intensity Range"], active=[0], width=145, margin=[10, 5, 0, 5]
)
main_auto_checkbox.on_click(main_auto_checkbox_callback)
main_auto_checkbox.on_change("active", main_auto_checkbox_callback)
def display_max_spinner_callback(_attr, _old, new):
lin_color_mapper.high = new
@ -709,8 +709,8 @@ def create():
display_min_spinner = Spinner(value=0, disabled=bool(main_auto_checkbox.active), width=100)
display_min_spinner.on_change("value", display_min_spinner_callback)
def proj_auto_checkbox_callback(state):
if state:
def proj_auto_checkbox_callback(_attr, _old, new):
if 0 in new:
proj_display_min_spinner.disabled = True
proj_display_max_spinner.disabled = True
else:
@ -722,7 +722,7 @@ def create():
proj_auto_checkbox = CheckboxGroup(
labels=["Projections Intensity Range"], active=[0], width=145, margin=[10, 5, 0, 5]
)
proj_auto_checkbox.on_click(proj_auto_checkbox_callback)
proj_auto_checkbox.on_change("active", proj_auto_checkbox_callback)
def proj_display_max_spinner_callback(_attr, _old, new):
lin_color_mapper_proj.high = new
@ -811,7 +811,7 @@ def create():
gamma = scan["gamma"][0]
omega = scan["omega"][0]
nu = scan["nu"][0]
nu = scan["nu"]
chi = scan["chi"][0]
phi = scan["phi"][0]
@ -842,10 +842,6 @@ def create():
x_pos = scan["fit"]["x_pos"]
y_pos = scan["fit"]["y_pos"]
if scan["zebra_mode"] == "nb":
chi = None
phi = None
events_data["wave"].append(wave)
events_data["ddist"].append(ddist)
events_data["cell"].append(cell)

View File

@ -209,8 +209,8 @@ def create():
plot = figure(
x_axis_label="Scan motor",
y_axis_label="Counts",
plot_height=450,
plot_width=700,
height=450,
width=700,
tools="pan,wheel_zoom,reset",
)
@ -243,8 +243,8 @@ def create():
ov_plot = figure(
x_axis_label="Scan motor",
y_axis_label="Counts",
plot_height=450,
plot_width=700,
height=450,
width=700,
tools="pan,wheel_zoom,reset",
)
@ -261,8 +261,8 @@ def create():
y_axis_label="Param",
x_range=Range1d(),
y_range=Range1d(),
plot_height=450,
plot_width=700,
height=450,
width=700,
tools="pan,wheel_zoom,reset",
)
@ -279,8 +279,8 @@ def create():
param_plot = figure(
x_axis_label="Parameter",
y_axis_label="Fit parameter",
plot_height=400,
plot_width=700,
height=400,
width=700,
tools="pan,wheel_zoom,reset",
)

View File

@ -290,8 +290,8 @@ def create():
plot = figure(
x_range=DataRange1d(),
y_range=DataRange1d(),
plot_height=550 + 27,
plot_width=550 + 117,
height=550 + 27,
width=550 + 117,
tools="pan,wheel_zoom,reset",
)
plot.toolbar.logo = None
@ -324,7 +324,7 @@ def create():
hkl_in_plane_y = TextInput(title="in-plane Y", value="", width=100, disabled=True)
def redef_lattice_cb_callback(_attr, _old, new):
if new:
if 0 in new:
redef_lattice_ti.disabled = False
else:
redef_lattice_ti.disabled = True
@ -334,7 +334,7 @@ def create():
redef_lattice_ti = TextInput(width=490, disabled=True)
def redef_ub_cb_callback(_attr, _old, new):
if new:
if 0 in new:
redef_ub_ti.disabled = False
else:
redef_ub_ti.disabled = True
@ -369,8 +369,8 @@ def create():
display_max_ni = NumericInput(title="max:", value=1, mode="float", width=70)
display_max_ni.on_change("value", display_max_ni_callback)
def colormap_scale_rg_callback(selection):
if selection == 0: # Linear
def colormap_scale_rg_callback(_attr, _old, new):
if new == 0: # Linear
plot_image.glyph.color_mapper = lin_color_mapper
lin_color_bar.visible = True
log_color_bar.visible = False
@ -384,7 +384,7 @@ def create():
colormap_scale_rg.active = 0
colormap_scale_rg = RadioGroup(labels=["Linear", "Logarithmic"], active=0, width=100)
colormap_scale_rg.on_click(colormap_scale_rg_callback)
colormap_scale_rg.on_change("active", colormap_scale_rg_callback)
xrange_min_ni = NumericInput(title="x range min:", value=0, mode="float", width=70)
xrange_max_ni = NumericInput(title="max:", value=1, mode="float", width=70)
@ -395,7 +395,7 @@ def create():
yrange_step_ni = NumericInput(title="y mesh:", value=0.01, mode="float", width=70)
def auto_range_cb_callback(_attr, _old, new):
if new:
if 0 in new:
xrange_min_ni.disabled = True
xrange_max_ni.disabled = True
yrange_min_ni.disabled = True

View File

@ -441,7 +441,7 @@ class PlotHKL:
plot_file = Button(label="Plot selected file(s)", button_type="primary", width=200)
plot_file.on_click(plot_file_callback)
plot = figure(plot_height=550, plot_width=550 + 32, tools="pan,wheel_zoom,reset")
plot = figure(height=550, width=550 + 32, tools="pan,wheel_zoom,reset")
plot.toolbar.logo = None
plot.xaxis.visible = False
@ -517,7 +517,7 @@ class PlotHKL:
tol_k_ni = NumericInput(title="k tolerance:", value=0.01, mode="float", width=100)
def show_legend_cb_callback(_attr, _old, new):
plot.legend.visible = bool(new)
plot.legend.visible = 0 in new
show_legend_cb = CheckboxGroup(labels=["Show legend"], active=[0])
show_legend_cb.on_change("active", show_legend_cb_callback)

View File

@ -8,41 +8,45 @@ import numpy as np
META_VARS_STR = (
"instrument",
"title",
"sample",
"comment",
"user",
"ProposalID",
"proposal_id",
"original_filename",
"date",
"zebra_mode",
"proposal",
"proposal_user",
"proposal_title",
"proposal_email",
"detectorDistance",
"sample_name",
)
META_VARS_FLOAT = (
"omega",
"mf",
"2-theta",
"chi",
"phi",
"nu",
"temp",
"wavelength",
"a",
"b",
"c",
"alpha",
"beta",
"gamma",
"omega",
"chi",
"phi",
"temp",
"mf",
"temperature",
"magnetic_field",
"cex1",
"cex2",
"wavelength",
"mexz",
"moml",
"mcvl",
"momu",
"mcvu",
"2-theta",
"twotheta",
"nu",
"gamma_angle",
"polar_angle",
"tilt_angle",
"distance",
"distance_an",
"snv",
"snh",
"snvm",
@ -55,6 +59,13 @@ META_VARS_FLOAT = (
"s2vb",
"s2hr",
"s2hl",
"a5",
"a6",
"a4t",
"s2ant",
"s2anb",
"s2anl",
"s2anr",
)
META_UB_MATRIX = ("ub1j", "ub2j", "ub3j", "UB")
@ -116,6 +127,10 @@ def parse_1D(fileobj, data_type):
var_name = var_name.strip()
value = value.strip()
if value == "UNKNOWN":
metadata[var_name] = None
continue
try:
if var_name in META_VARS_STR:
metadata[var_name] = value
@ -123,6 +138,10 @@ def parse_1D(fileobj, data_type):
elif var_name in META_VARS_FLOAT:
if var_name == "2-theta": # fix that angle name not to be an expression
var_name = "twotheta"
if var_name == "temperature":
var_name = "temp"
if var_name == "magnetic_field":
var_name = "mf"
if var_name in ("a", "b", "c", "alpha", "beta", "gamma"):
var_name += "_cell"
metadata[var_name] = float(value)
@ -202,9 +221,12 @@ def parse_1D(fileobj, data_type):
dataset.append({**metadata, **scan})
elif data_type == ".dat":
# TODO: this might need to be adapted in the future, when "gamma" will be added to dat files
if metadata["zebra_mode"] == "nb":
metadata["gamma"] = metadata["twotheta"]
if "gamma_angle" in metadata:
# support for the new format
metadata["gamma"] = metadata["gamma_angle"]
else:
metadata["gamma"] = metadata["twotheta"]
scan = defaultdict(list)
scan["export"] = True

View File

@ -34,7 +34,7 @@ def normalize_dataset(dataset, monitor=100_000):
def merge_duplicates(dataset):
merged = np.zeros(len(dataset), dtype=np.bool)
merged = np.zeros(len(dataset), dtype=bool)
for ind_into, scan_into in enumerate(dataset):
for ind_from, scan_from in enumerate(dataset[ind_into + 1 :], start=ind_into + 1):
if _parameters_match(scan_into, scan_from) and not merged[ind_from]:
@ -82,7 +82,7 @@ def merge_datasets(dataset_into, dataset_from):
print(f"Scan motors mismatch between datasets: {scan_motors_into} vs {scan_motors_from}")
return
merged = np.zeros(len(dataset_from), dtype=np.bool)
merged = np.zeros(len(dataset_from), dtype=bool)
for scan_into in dataset_into:
for ind, scan_from in enumerate(dataset_from):
if _parameters_match(scan_into, scan_from) and not merged[ind]:

View File

@ -47,9 +47,9 @@ def parse_h5meta(file):
if variable in META_STR:
pass
elif variable in META_CELL:
value = np.array(value.split(",")[:6], dtype=np.float)
value = np.array(value.split(",")[:6], dtype=float)
elif variable in META_MATRIX:
value = np.array(value.split(",")[:9], dtype=np.float).reshape(3, 3)
value = np.array(value.split(",")[:9], dtype=float).reshape(3, 3)
else: # default is a single float number
value = float(value)
content[section][variable] = value
@ -69,7 +69,7 @@ def read_detector_data(filepath, cami_meta=None):
ndarray: A 3D array of data, omega, gamma, nu.
"""
with h5py.File(filepath, "r") as h5f:
counts = h5f["/entry1/area_detector2/data"][:].astype(np.float64)
counts = h5f["/entry1/area_detector2/data"][:].astype(float)
n, cols, rows = counts.shape
if "/entry1/experiment_identifier" in h5f: # old format
@ -114,10 +114,14 @@ def read_detector_data(filepath, cami_meta=None):
scan["nu"] = h5f["/entry1/ZEBRA/area_detector2/tilt_angle"][0]
scan["ddist"] = h5f["/entry1/ZEBRA/area_detector2/distance"][0]
scan["wave"] = h5f["/entry1/ZEBRA/monochromator/wavelength"][0]
scan["chi"] = h5f["/entry1/sample/chi"][:]
if scan["zebra_mode"] == "nb":
scan["chi"] = np.array([180])
scan["phi"] = np.array([0])
elif scan["zebra_mode"] == "bi":
scan["chi"] = h5f["/entry1/sample/chi"][:]
scan["phi"] = h5f["/entry1/sample/phi"][:]
if len(scan["chi"]) == 1:
scan["chi"] = np.ones(n) * scan["chi"]
scan["phi"] = h5f["/entry1/sample/phi"][:]
if len(scan["phi"]) == 1:
scan["phi"] = np.ones(n) * scan["phi"]
if h5f["/entry1/sample/UB"].size == 0: