diff --git a/specsanalyzer/latest/_modules/index.html b/specsanalyzer/latest/_modules/index.html index ef73a53..1a4734d 100644 --- a/specsanalyzer/latest/_modules/index.html +++ b/specsanalyzer/latest/_modules/index.html @@ -7,7 +7,7 @@
-specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
diff --git a/specsanalyzer/latest/_modules/specsanalyzer/config.html b/specsanalyzer/latest/_modules/specsanalyzer/config.html index 46ffdac..354b898 100644 --- a/specsanalyzer/latest/_modules/specsanalyzer/config.html +++ b/specsanalyzer/latest/_modules/specsanalyzer/config.html @@ -7,7 +7,7 @@ -specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -551,22 +551,22 @@
"""This module contains a config library for loading yaml/json files into dicts"""
-from __future__ import annotations
+from __future__ import annotations
-import json
-import os
-import platform
-from importlib.util import find_spec
-from pathlib import Path
+import json
+import os
+import platform
+from importlib.util import find_spec
+from pathlib import Path
-import yaml
+import yaml
package_dir = os.path.dirname(find_spec("specsanalyzer").origin)
[docs]
-def parse_config(
+def parse_config(
config: dict | str = None,
folder_config: dict | str = None,
user_config: dict | str = None,
@@ -694,7 +694,7 @@ Source code for specsanalyzer.config
[docs]
-def load_config(config_path: str) -> dict:
+def load_config(config_path: str) -> dict:
"""Loads config parameter files.
Args:
@@ -728,7 +728,7 @@ Source code for specsanalyzer.config
[docs]
-def save_config(config_dict: dict, config_path: str, overwrite: bool = False):
+def save_config(config_dict: dict, config_path: str, overwrite: bool = False):
"""Function to save a given config dictionary to a json or yaml file. Normally, it loads any
existing file of the given name, and keeps any existing dictionary keys not present in the
provided dictionary. The overwrite option creates a fully empty dictionary first.
@@ -761,7 +761,7 @@ Source code for specsanalyzer.config
[docs]
-def complete_dictionary(dictionary: dict, base_dictionary: dict) -> dict:
+def complete_dictionary(dictionary: dict, base_dictionary: dict) -> dict:
"""Iteratively completes a dictionary from a base dictionary, by adding keys that are missing
in the dictionary, and are present in the base dictionary.
diff --git a/specsanalyzer/latest/_modules/specsanalyzer/convert.html b/specsanalyzer/latest/_modules/specsanalyzer/convert.html
index 3df1dbd..819e7c5 100644
--- a/specsanalyzer/latest/_modules/specsanalyzer/convert.html
+++ b/specsanalyzer/latest/_modules/specsanalyzer/convert.html
@@ -7,7 +7,7 @@
- specsanalyzer.convert — specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer.convert — specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -29,7 +29,7 @@
-
+
@@ -37,7 +37,7 @@
-
+
@@ -46,7 +46,7 @@
@@ -54,7 +54,7 @@
-
+
@@ -116,7 +116,7 @@
- specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -551,15 +551,15 @@
Source code for specsanalyzer.convert
"""Specsanalyzer image conversion module"""
-from __future__ import annotations
+from __future__ import annotations
-import numpy as np
-from scipy.ndimage import map_coordinates
+import numpy as np
+from scipy.ndimage import map_coordinates
[docs]
-def get_damatrix_from_calib2d(
+def get_damatrix_from_calib2d(
lens_mode: str,
kinetic_energy: float,
pass_energy: float,
@@ -594,7 +594,7 @@ Source code for specsanalyzer.convert
except KeyError as exc:
raise KeyError(
"The supported modes were not found in the calib2d dictionary",
- ) from exc
+ ) from exc
if lens_mode in supported_angle_modes:
# given the lens mode get all the retardation ratios available
@@ -653,7 +653,7 @@ Source code for specsanalyzer.convert
[docs]
-def bisection(array: np.ndarray, value: float) -> int:
+def bisection(array: np.ndarray, value: float) -> int:
"""
Auxiliary function to find the closest rr index from https://stackoverflow.com/questions/2566412/
find-nearest-value-in-numpy-array
@@ -697,7 +697,7 @@ Source code for specsanalyzer.convert
[docs]
-def second_closest_rr(rrvec: np.ndarray, closest_rr_index: int) -> int:
+def second_closest_rr(rrvec: np.ndarray, closest_rr_index: int) -> int:
"""Return closest_rr_index+1 unless you are at the edge of the rrvec.
Args:
@@ -719,7 +719,7 @@ Source code for specsanalyzer.convert
[docs]
-def get_rr_da(
+def get_rr_da(
lens_mode: str,
calib2d_dict: dict,
) -> tuple[np.ndarray, np.ndarray]:
@@ -748,7 +748,7 @@ Source code for specsanalyzer.convert
except KeyError as exc:
raise KeyError(
"The supported modes were not found in the calib2d dictionary",
- ) from exc
+ ) from exc
if lens_mode in supported_angle_modes:
rr_array = np.array(list(calib2d_dict[lens_mode]["rr"]))
@@ -762,7 +762,7 @@ Source code for specsanalyzer.convert
except KeyError as exc:
raise ValueError(
"Da values do not exist for the given mode.",
- ) from exc
+ ) from exc
da_matrix = np.zeros([dim1, dim2, dim3])
for count, item in enumerate(rr_array):
@@ -796,7 +796,7 @@ Source code for specsanalyzer.convert
[docs]
-def calculate_polynomial_coef_da(
+def calculate_polynomial_coef_da(
da_matrix: np.ndarray,
kinetic_energy: float,
pass_energy: float,
@@ -838,7 +838,7 @@ Source code for specsanalyzer.convert
[docs]
-def zinner(
+def zinner(
kinetic_energy: np.ndarray,
angle: np.ndarray,
da_poly_matrix: np.ndarray,
@@ -869,7 +869,7 @@ Source code for specsanalyzer.convert
[docs]
-def zinner_diff(
+def zinner_diff(
kinetic_energy: np.ndarray,
angle: np.ndarray,
da_poly_matrix: np.ndarray,
@@ -904,7 +904,7 @@ Source code for specsanalyzer.convert
[docs]
-def mcp_position_mm(
+def mcp_position_mm(
kinetic_energy: np.ndarray,
angle: np.ndarray,
a_inner: float,
@@ -945,7 +945,7 @@ Source code for specsanalyzer.convert
[docs]
-def calculate_matrix_correction(
+def calculate_matrix_correction(
kinetic_energy: float,
pass_energy: float,
nx_pixels: int,
@@ -1039,7 +1039,7 @@ Source code for specsanalyzer.convert
[docs]
-def calculate_jacobian(
+def calculate_jacobian(
angular_correction_matrix: np.ndarray,
e_correction: np.ndarray,
ek_axis: np.ndarray,
@@ -1067,7 +1067,7 @@ Source code for specsanalyzer.convert
[docs]
-def physical_unit_data(
+def physical_unit_data(
image: np.ndarray,
angular_correction_matrix: np.ndarray,
e_correction: float,
diff --git a/specsanalyzer/latest/_modules/specsanalyzer/core.html b/specsanalyzer/latest/_modules/specsanalyzer/core.html
index bc04951..2992396 100644
--- a/specsanalyzer/latest/_modules/specsanalyzer/core.html
+++ b/specsanalyzer/latest/_modules/specsanalyzer/core.html
@@ -7,7 +7,7 @@
- specsanalyzer.core — specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer.core — specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -29,7 +29,7 @@
-
+
@@ -37,7 +37,7 @@
-
+
@@ -46,7 +46,7 @@
@@ -54,7 +54,7 @@
-
+
@@ -116,7 +116,7 @@
- specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -551,35 +551,35 @@
Source code for specsanalyzer.core
"""This is the specsanalyzer core class"""
-from __future__ import annotations
-
-import os
-from typing import Any
-from typing import Generator
-
-import imutils
-import ipywidgets as ipw
-import matplotlib
-import matplotlib.pyplot as plt
-import numpy as np
-import xarray as xr
-from IPython.display import display
-
-from specsanalyzer import io
-from specsanalyzer.config import complete_dictionary
-from specsanalyzer.config import parse_config
-from specsanalyzer.convert import calculate_matrix_correction
-from specsanalyzer.convert import get_damatrix_from_calib2d
-from specsanalyzer.convert import physical_unit_data
-from specsanalyzer.img_tools import crop_xarray
-from specsanalyzer.img_tools import fourier_filter_2d
+from __future__ import annotations
+
+import os
+from typing import Any
+from typing import Generator
+
+import imutils
+import ipywidgets as ipw
+import matplotlib
+import matplotlib.pyplot as plt
+import numpy as np
+import xarray as xr
+from IPython.display import display
+
+from specsanalyzer import io
+from specsanalyzer.config import complete_dictionary
+from specsanalyzer.config import parse_config
+from specsanalyzer.convert import calculate_matrix_correction
+from specsanalyzer.convert import get_damatrix_from_calib2d
+from specsanalyzer.convert import physical_unit_data
+from specsanalyzer.img_tools import crop_xarray
+from specsanalyzer.img_tools import fourier_filter_2d
package_dir = os.path.dirname(__file__)
[docs]
-class SpecsAnalyzer:
+class SpecsAnalyzer:
"""SpecsAnalyzer: A class to convert photoemission data from a SPECS Phoibos analyzer from
camera image coordinates into physical units (energy, angle, position).
@@ -589,7 +589,7 @@ Source code for specsanalyzer.core
**kwds: Keyword arguments passed to ``parse_config``.
"""
- def __init__(
+ def __init__(
self,
metadata: dict[Any, Any] = {},
config: dict[Any, Any] | str = {},
@@ -619,7 +619,7 @@ Source code for specsanalyzer.core
self._correction_matrix_dict: dict[Any, Any] = {}
- def __repr__(self):
+ def __repr__(self):
if self._config is None:
pretty_str = "No configuration available"
else:
@@ -630,23 +630,23 @@ Source code for specsanalyzer.core
return pretty_str if pretty_str is not None else ""
@property
- def config(self) -> dict:
+ def config(self) -> dict:
"""Get config"""
return self._config
@property
- def calib2d(self) -> dict:
+ def calib2d(self) -> dict:
"""Get calib2d dict"""
return self._calib2d
@property
- def correction_matrix_dict(self) -> dict:
+ def correction_matrix_dict(self) -> dict:
"""Get correction_matrix_dict"""
return self._correction_matrix_dict
[docs]
- def convert_image(
+ def convert_image(
self,
raw_img: np.ndarray,
lens_mode: str,
@@ -914,7 +914,7 @@ Source code for specsanalyzer.core
[docs]
- def crop_tool(
+ def crop_tool(
self,
raw_img: np.ndarray,
lens_mode: str,
@@ -1053,7 +1053,7 @@ Source code for specsanalyzer.core
max=data_array.data.max(),
)
- def update(hline, vline, v_vals):
+ def update(hline, vline, v_vals):
lineh1.set_ydata([hline[0]])
lineh2.set_ydata([hline[1]])
linev1.set_xdata([vline[0]])
@@ -1068,7 +1068,7 @@ Source code for specsanalyzer.core
v_vals=clim_slider,
)
- def cropit(val): # pylint: disable=unused-argument
+ def cropit(val): # pylint: disable=unused-argument
ang_min = min(hline_slider.value)
ang_max = max(hline_slider.value)
ek_min = min(vline_slider.value)
@@ -1131,7 +1131,7 @@ Source code for specsanalyzer.core
[docs]
- def fft_tool(
+ def fft_tool(
self,
raw_image: np.ndarray,
apply: bool = False,
@@ -1252,7 +1252,7 @@ Source code for specsanalyzer.core
max=int(np.log10(np.abs(img).max())) + 1,
)
- def update(v_vals, pos_x, pos_y, sigma_x, sigma_y, amplitude):
+ def update(v_vals, pos_x, pos_y, sigma_x, sigma_y, amplitude):
fft_filter_peaks = create_fft_params(amplitude, pos_x, pos_y, sigma_x, sigma_y)
msk = fourier_filter_2d(raw_image, peaks=fft_filter_peaks, ret="mask")
filtered_new = fourier_filter_2d(raw_image, peaks=fft_filter_peaks, ret="filtered")
@@ -1289,7 +1289,7 @@ Source code for specsanalyzer.core
v_vals=clim_slider,
)
- def apply_fft(apply: bool): # pylint: disable=unused-argument
+ def apply_fft(apply: bool): # pylint: disable=unused-argument
amplitude = amplitude_slider.value
pos_x = pos_x_slider.value
pos_y = pos_y_slider.value
@@ -1329,7 +1329,7 @@ Source code for specsanalyzer.core
[docs]
-def create_fft_params(
+def create_fft_params(
amplitude: float,
pos_x: float,
pos_y: float,
diff --git a/specsanalyzer/latest/_modules/specsanalyzer/img_tools.html b/specsanalyzer/latest/_modules/specsanalyzer/img_tools.html
index e1f4b2d..e07eef1 100644
--- a/specsanalyzer/latest/_modules/specsanalyzer/img_tools.html
+++ b/specsanalyzer/latest/_modules/specsanalyzer/img_tools.html
@@ -7,7 +7,7 @@
- specsanalyzer.img_tools — specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer.img_tools — specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -29,7 +29,7 @@
-
+
@@ -37,7 +37,7 @@
-
+
@@ -46,7 +46,7 @@
@@ -54,7 +54,7 @@
-
+
@@ -116,7 +116,7 @@
- specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -551,17 +551,17 @@
Source code for specsanalyzer.img_tools
"""This module contains image manipulation tools for the specsanalyzer package"""
-from __future__ import annotations
+from __future__ import annotations
-from typing import Sequence
+from typing import Sequence
-import numpy as np
-import xarray as xr
+import numpy as np
+import xarray as xr
[docs]
-def gauss2d(
+def gauss2d(
x: float | np.ndarray,
y: float | np.ndarray,
mx: float,
@@ -592,7 +592,7 @@ Source code for specsanalyzer.img_tools
[docs]
-def fourier_filter_2d(
+def fourier_filter_2d(
image: np.ndarray,
peaks: Sequence[dict],
ret: str = "filtered",
@@ -641,7 +641,7 @@ Source code for specsanalyzer.img_tools
raise KeyError(
f"The peaks input is supposed to be a list of dicts with the "
"following structure: pos_x, pos_y, sigma_x, sigma_y, amplitude.",
- ) from exc
+ ) from exc
# apply mask to the FFT, and transform back
filtered = np.fft.irfft2(np.fft.ifftshift(image_fft * mask, axes=0))
@@ -661,7 +661,7 @@ Source code for specsanalyzer.img_tools
[docs]
-def crop_xarray(
+def crop_xarray(
data_array: xr.DataArray,
x_min: float,
x_max: float,
diff --git a/specsanalyzer/latest/_modules/specsanalyzer/io.html b/specsanalyzer/latest/_modules/specsanalyzer/io.html
index d219e61..2dd2be3 100644
--- a/specsanalyzer/latest/_modules/specsanalyzer/io.html
+++ b/specsanalyzer/latest/_modules/specsanalyzer/io.html
@@ -7,7 +7,7 @@
- specsanalyzer.io — specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer.io — specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -29,7 +29,7 @@
-
+
@@ -37,7 +37,7 @@
-
+
@@ -46,7 +46,7 @@
@@ -54,7 +54,7 @@
-
+
@@ -116,7 +116,7 @@
- specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -551,17 +551,17 @@
Source code for specsanalyzer.io
"""This module contains file input/output functions for the specsanalyzer module"""
-from __future__ import annotations
+from __future__ import annotations
-from pathlib import Path
-from typing import Any
-from typing import Sequence
+from pathlib import Path
+from typing import Any
+from typing import Sequence
-import h5py
-import numpy as np
-import tifffile
-import xarray as xr
-from pynxtools.dataconverter.convert import convert
+import h5py
+import numpy as np
+import tifffile
+import xarray as xr
+from pynxtools.dataconverter.convert import convert
_IMAGEJ_DIMS_ORDER = "TZCYXS"
_IMAGEJ_DIMS_ALIAS = {
@@ -591,7 +591,7 @@ Source code for specsanalyzer.io
[docs]
-def recursive_write_metadata(h5group: h5py.Group, node: dict):
+def recursive_write_metadata(h5group: h5py.Group, node: dict):
"""Recurses through a python dictionary and writes it into an hdf5 file.
Args:
@@ -631,13 +631,13 @@ Source code for specsanalyzer.io
except BaseException as exc:
raise ValueError(
f"Unknown error occurred, cannot save {item} of type {type(item)}.",
- ) from exc
+ ) from exc
[docs]
-def recursive_parse_metadata(
+def recursive_parse_metadata(
node: h5py.Group | h5py.Dataset,
) -> dict:
"""Recurses through an hdf5 file, and parse it into a dictionary.
@@ -668,7 +668,7 @@ Source code for specsanalyzer.io
[docs]
-def to_h5(data: xr.DataArray, faddr: str, mode: str = "w"):
+def to_h5(data: xr.DataArray, faddr: str, mode: str = "w"):
"""Save xarray formatted data to hdf5
Args:
@@ -720,7 +720,7 @@ Source code for specsanalyzer.io
[docs]
-def load_h5(faddr: str, mode: str = "r") -> xr.DataArray:
+def load_h5(faddr: str, mode: str = "r") -> xr.DataArray:
"""Read xarray data from formatted hdf5 file
Args:
@@ -737,7 +737,7 @@ Source code for specsanalyzer.io
except KeyError as exc:
raise ValueError(
f"Wrong Data Format, the BinnedData were not found. The error was{exc}.",
- ) from exc
+ ) from exc
# Reading the axes
bin_axes = []
@@ -750,7 +750,7 @@ Source code for specsanalyzer.io
except KeyError as exc:
raise ValueError(
f"Wrong Data Format, the axes were not found. The error was {exc}",
- ) from exc
+ ) from exc
# load metadata
metadata = None
@@ -780,7 +780,7 @@ Source code for specsanalyzer.io
[docs]
-def to_tiff(
+def to_tiff(
data: xr.DataArray | np.ndarray,
faddr: Path | str,
alias_dict: dict = None,
@@ -845,7 +845,7 @@ Source code for specsanalyzer.io
[docs]
-def _sort_dims_for_imagej(dims: list, alias_dict: dict = None) -> list:
+def _sort_dims_for_imagej(dims: list, alias_dict: dict = None) -> list:
"""Guess the order of the dimensions from the alias dictionary
Args:
@@ -871,7 +871,7 @@ Source code for specsanalyzer.io
[docs]
-def _fill_missing_dims(dims: list, alias_dict: dict = None) -> list:
+def _fill_missing_dims(dims: list, alias_dict: dict = None) -> list:
"""Guess the order of the dimensions from the alias dictionary
Args:
@@ -925,7 +925,7 @@ Source code for specsanalyzer.io
[docs]
-def load_tiff(
+def load_tiff(
faddr: str | Path,
coords: dict = None,
dims: Sequence = None,
@@ -975,7 +975,7 @@ Source code for specsanalyzer.io
[docs]
-def to_nexus(
+def to_nexus(
data: xr.DataArray,
faddr: str,
reader: str,
@@ -1014,7 +1014,7 @@ Source code for specsanalyzer.io
[docs]
-def get_pair_from_list(list_line: list) -> list:
+def get_pair_from_list(list_line: list) -> list:
"""Returns key value pair for the read function
where a line in the file contains '=' character.
@@ -1047,7 +1047,7 @@ Source code for specsanalyzer.io
[docs]
-def read_calib2d(filepath: str) -> list:
+def read_calib2d(filepath: str) -> list:
"""Reads the calib2d file into a convenient list for the parser
function containing useful and cleaned data.
@@ -1090,7 +1090,7 @@ Source code for specsanalyzer.io
[docs]
-def parse_calib2d_to_dict(filepath: str) -> dict:
+def parse_calib2d_to_dict(filepath: str) -> dict:
"""Parses the given calib2d file into a nested dictionary structure
to provide parameters for image conversion.
@@ -1133,7 +1133,7 @@ Source code for specsanalyzer.io
[docs]
-def get_modes_from_calib_dict(calib_dict: dict) -> tuple[list, list]:
+def get_modes_from_calib_dict(calib_dict: dict) -> tuple[list, list]:
"""create a list of supported modes, divided in spatial and angular modes
Args:
diff --git a/specsanalyzer/latest/_modules/specsscan/core.html b/specsanalyzer/latest/_modules/specsscan/core.html
index 28631c1..3f76eab 100644
--- a/specsanalyzer/latest/_modules/specsscan/core.html
+++ b/specsanalyzer/latest/_modules/specsscan/core.html
@@ -7,7 +7,7 @@
- specsscan.core — specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsscan.core — specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -29,7 +29,7 @@
-
+
@@ -37,7 +37,7 @@
-
+
@@ -46,7 +46,7 @@
@@ -54,7 +54,7 @@
-
+
@@ -116,7 +116,7 @@
- specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -551,33 +551,33 @@
Source code for specsscan.core
"""This is the SpecsScan core class"""
-from __future__ import annotations
-
-import copy
-import os
-import pathlib
-from importlib.util import find_spec
-from logging import warn
-from pathlib import Path
-from typing import Any
-from typing import Sequence
-
-import matplotlib
-import numpy as np
-import xarray as xr
-from tqdm.auto import tqdm
-
-from specsanalyzer import SpecsAnalyzer
-from specsanalyzer.config import parse_config
-from specsanalyzer.io import to_h5
-from specsanalyzer.io import to_nexus
-from specsanalyzer.io import to_tiff
-from specsscan.helpers import get_coords
-from specsscan.helpers import get_scan_path
-from specsscan.helpers import handle_meta
-from specsscan.helpers import load_images
-from specsscan.helpers import parse_info_to_dict
-from specsscan.helpers import parse_lut_to_df
+from __future__ import annotations
+
+import copy
+import os
+import pathlib
+from importlib.util import find_spec
+from logging import warn
+from pathlib import Path
+from typing import Any
+from typing import Sequence
+
+import matplotlib
+import numpy as np
+import xarray as xr
+from tqdm.auto import tqdm
+
+from specsanalyzer import SpecsAnalyzer
+from specsanalyzer.config import parse_config
+from specsanalyzer.io import to_h5
+from specsanalyzer.io import to_nexus
+from specsanalyzer.io import to_tiff
+from specsscan.helpers import get_coords
+from specsscan.helpers import get_scan_path
+from specsscan.helpers import handle_meta
+from specsscan.helpers import load_images
+from specsscan.helpers import parse_info_to_dict
+from specsscan.helpers import parse_lut_to_df
package_dir = os.path.dirname(find_spec("specsscan").origin)
@@ -585,7 +585,7 @@ Source code for specsscan.core
[docs]
-class SpecsScan:
+class SpecsScan:
"""SpecsAnalyzer class for loading scans and data from SPECS Phoibos electron analyzers,
generated with the ARPESControl software at Fritz Haber Institute, Berlin, and EPFL, Lausanne.
@@ -595,7 +595,7 @@ Source code for specsscan.core
**kwds: Keyword arguments passed to ``parse_config``.
"""
- def __init__(
+ def __init__(
self,
metadata: dict = {},
config: dict | str = {},
@@ -635,7 +635,7 @@ Source code for specsscan.core
self._result: xr.DataArray = None
# pylint: disable=duplicate-code
- def __repr__(self):
+ def __repr__(self):
if self._config is None:
pretty_str = "No configuration available"
else:
@@ -646,12 +646,12 @@ Source code for specsscan.core
return pretty_str if pretty_str is not None else ""
@property
- def config(self):
+ def config(self):
"""Get config"""
return self._config
@config.setter
- def config(self, config: dict | str):
+ def config(self, config: dict | str):
"""Set config"""
self._config = parse_config(
config,
@@ -663,13 +663,13 @@ Source code for specsscan.core
self.spa = SpecsAnalyzer()
@property
- def result(self):
+ def result(self):
"""Get result xarray"""
return self._result
[docs]
- def load_scan(
+ def load_scan(
self,
scan: int,
path: str | Path = "",
@@ -812,10 +812,10 @@ Source code for specsscan.core
"/entry/sample/transformations/sample_azimuth": "Azimuth",
}
- # store link information for resolved axis coordinates
+ # store data for resolved axis coordinates
for k, v in depends_dict.items():
if v in axis_dict:
- self._scan_info[axis_dict[v]] = "@link:/entry/data/" + k
+ self._scan_info[axis_dict[v]] = res_xarray.coords[k].data
for name in res_xarray.dims:
try:
@@ -846,7 +846,7 @@ Source code for specsscan.core
[docs]
- def crop_tool(self, scan: int = None, path: Path | str = "", **kwds):
+ def crop_tool(self, scan: int = None, path: Path | str = "", **kwds):
"""Cropping tool interface to crop_tool method of the SpecsAnalyzer class.
Args:
@@ -871,7 +871,7 @@ Source code for specsscan.core
try:
image = self.metadata["loader"]["raw_data"][0]
except KeyError as exc:
- raise ValueError("No image loaded, load image first!") from exc
+ raise ValueError("No image loaded, load image first!") from exc
self.spa.crop_tool(
image,
@@ -885,7 +885,7 @@ Source code for specsscan.core
[docs]
- def fft_tool(self, scan: int = None, path: Path | str = "", **kwds):
+ def fft_tool(self, scan: int = None, path: Path | str = "", **kwds):
"""FFT tool to play around with the peak parameters in the Fourier plane. Built to filter
out the meshgrid appearing in the raw data images. The optimized parameters are stored in
the class config dict under fft_filter_peaks.
@@ -915,7 +915,7 @@ Source code for specsscan.core
try:
image = self.metadata["loader"]["raw_data"][0]
except KeyError as exc:
- raise ValueError("No image loaded, load image first!") from exc
+ raise ValueError("No image loaded, load image first!") from exc
self.spa.fft_tool(
image,
@@ -925,7 +925,7 @@ Source code for specsscan.core
[docs]
- def check_scan(
+ def check_scan(
self,
scan: int,
delays: Sequence[int] | int,
@@ -1054,7 +1054,7 @@ Source code for specsscan.core
[docs]
- def save(
+ def save(
self,
faddr: str,
**kwds,
@@ -1140,7 +1140,7 @@ Source code for specsscan.core
[docs]
- def process_sweep_scan(
+ def process_sweep_scan(
self,
raw_data: list[np.ndarray],
kinetic_energy: np.ndarray,
diff --git a/specsanalyzer/latest/_modules/specsscan/helpers.html b/specsanalyzer/latest/_modules/specsscan/helpers.html
index c57255f..e239268 100644
--- a/specsanalyzer/latest/_modules/specsscan/helpers.html
+++ b/specsanalyzer/latest/_modules/specsscan/helpers.html
@@ -7,7 +7,7 @@
- specsscan.helpers — specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsscan.helpers — specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -29,7 +29,7 @@
-
+
@@ -37,7 +37,7 @@
-
+
@@ -46,7 +46,7 @@
@@ -54,7 +54,7 @@
-
+
@@ -116,7 +116,7 @@
- specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -551,27 +551,27 @@
Source code for specsscan.helpers
"""This script contains helper functions used by the specsscan class"""
-from __future__ import annotations
+from __future__ import annotations
-import datetime as dt
-import json
-from pathlib import Path
-from typing import Any
-from typing import Sequence
-from urllib.error import HTTPError
-from urllib.error import URLError
-from urllib.request import urlopen
+import datetime as dt
+import json
+from pathlib import Path
+from typing import Any
+from typing import Sequence
+from urllib.error import HTTPError
+from urllib.error import URLError
+from urllib.request import urlopen
-import numpy as np
-import pandas as pd
-from tqdm.auto import tqdm
+import numpy as np
+import pandas as pd
+from tqdm.auto import tqdm
-from specsanalyzer.config import complete_dictionary
+from specsanalyzer.config import complete_dictionary
[docs]
-def get_scan_path(path: Path | str, scan: int, basepath: Path | str) -> Path:
+def get_scan_path(path: Path | str, scan: int, basepath: Path | str) -> Path:
"""Returns the path to the given scan.
Args:
@@ -607,7 +607,7 @@ Source code for specsscan.helpers
[docs]
-def load_images(
+def load_images(
scan_path: Path,
df_lut: pd.DataFrame = None,
iterations: np.ndarray | slice | Sequence[int] | Sequence[slice] = None,
@@ -681,7 +681,7 @@ Source code for specsscan.helpers
"the chosen data. In case of a single scan, "
f"try without passing iterations inside the "
"load_scan method.",
- ) from exc
+ ) from exc
print(f"Averaging over {avg_dim}...")
for dim in tqdm(raw_2d_sliced):
@@ -718,7 +718,7 @@ Source code for specsscan.helpers
[docs]
-def get_raw2d(scan_list: list[str], raw_array: np.ndarray) -> np.ndarray:
+def get_raw2d(scan_list: list[str], raw_array: np.ndarray) -> np.ndarray:
"""Converts a 1-D array of raw scan names into 2-D based on the number of iterations
Args:
@@ -762,7 +762,7 @@ Source code for specsscan.helpers
[docs]
-def parse_lut_to_df(scan_path: Path) -> pd.DataFrame:
+def parse_lut_to_df(scan_path: Path) -> pd.DataFrame:
"""Loads the contents of LUT.txt file into a pandas data frame to be used as metadata.
Args:
@@ -794,7 +794,7 @@ Source code for specsscan.helpers
[docs]
-def get_coords(
+def get_coords(
scan_path: Path,
scan_type: str,
scan_info: dict[Any, Any],
@@ -842,7 +842,7 @@ Source code for specsscan.helpers
dim = df_new.columns[index]
else:
- raise FileNotFoundError("scanvector.txt file not found!") from exc
+ raise FileNotFoundError("scanvector.txt file not found!") from exc
if scan_type == "delay":
t_0 = scan_info["TimeZero"]
@@ -855,7 +855,7 @@ Source code for specsscan.helpers
[docs]
-def compare_coords(axis_data: np.ndarray) -> tuple[np.ndarray, int]:
+def compare_coords(axis_data: np.ndarray) -> tuple[np.ndarray, int]:
"""Identifies the most changing column in a given 2-D numpy array.
Args:
@@ -881,7 +881,7 @@ Source code for specsscan.helpers
[docs]
-def parse_info_to_dict(path: Path) -> dict:
+def parse_info_to_dict(path: Path) -> dict:
"""Parses the contents of info.txt file into a dictionary
Args:
@@ -911,7 +911,7 @@ Source code for specsscan.helpers
info_dict[key] = value
except FileNotFoundError as exc:
- raise FileNotFoundError("info.txt file not found.") from exc
+ raise FileNotFoundError("info.txt file not found.") from exc
return info_dict
@@ -919,7 +919,7 @@ Source code for specsscan.helpers
[docs]
-def handle_meta(
+def handle_meta(
df_lut: pd.DataFrame,
scan_info: dict,
config: dict,
@@ -1062,7 +1062,7 @@ Source code for specsscan.helpers
[docs]
-def get_archiver_data(
+def get_archiver_data(
archiver_url: str,
archiver_channel: str,
ts_from: float,
@@ -1093,7 +1093,7 @@ Source code for specsscan.helpers
[docs]
-def find_scan(path: Path, scan: int) -> list[Path]:
+def find_scan(path: Path, scan: int) -> list[Path]:
"""Search function to locate the scan folder
Args:
@@ -1127,7 +1127,7 @@ Source code for specsscan.helpers
[docs]
-def find_scan_type(
+def find_scan_type(
path: Path,
scan_type: str,
):
diff --git a/specsanalyzer/latest/_static/documentation_options.js b/specsanalyzer/latest/_static/documentation_options.js
index 5543657..8493108 100644
--- a/specsanalyzer/latest/_static/documentation_options.js
+++ b/specsanalyzer/latest/_static/documentation_options.js
@@ -1,5 +1,5 @@
const DOCUMENTATION_OPTIONS = {
- VERSION: '0.5.1.dev2+g5d28e05',
+ VERSION: '0.5.1.dev10+g0c6ed22',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
diff --git a/specsanalyzer/latest/_static/pygments.css b/specsanalyzer/latest/_static/pygments.css
index 012e6a0..d7dd577 100644
--- a/specsanalyzer/latest/_static/pygments.css
+++ b/specsanalyzer/latest/_static/pygments.css
@@ -6,11 +6,11 @@ html[data-theme="light"] .highlight span.linenos.special { color: #000000; backg
html[data-theme="light"] .highlight .hll { background-color: #fae4c2 }
html[data-theme="light"] .highlight { background: #fefefe; color: #080808 }
html[data-theme="light"] .highlight .c { color: #515151 } /* Comment */
-html[data-theme="light"] .highlight .err { color: #a12236 } /* Error */
-html[data-theme="light"] .highlight .k { color: #6730c5 } /* Keyword */
-html[data-theme="light"] .highlight .l { color: #7f4707 } /* Literal */
+html[data-theme="light"] .highlight .err { color: #A12236 } /* Error */
+html[data-theme="light"] .highlight .k { color: #6730C5 } /* Keyword */
+html[data-theme="light"] .highlight .l { color: #7F4707 } /* Literal */
html[data-theme="light"] .highlight .n { color: #080808 } /* Name */
-html[data-theme="light"] .highlight .o { color: #00622f } /* Operator */
+html[data-theme="light"] .highlight .o { color: #00622F } /* Operator */
html[data-theme="light"] .highlight .p { color: #080808 } /* Punctuation */
html[data-theme="light"] .highlight .ch { color: #515151 } /* Comment.Hashbang */
html[data-theme="light"] .highlight .cm { color: #515151 } /* Comment.Multiline */
@@ -18,135 +18,135 @@ html[data-theme="light"] .highlight .cp { color: #515151 } /* Comment.Preproc */
html[data-theme="light"] .highlight .cpf { color: #515151 } /* Comment.PreprocFile */
html[data-theme="light"] .highlight .c1 { color: #515151 } /* Comment.Single */
html[data-theme="light"] .highlight .cs { color: #515151 } /* Comment.Special */
-html[data-theme="light"] .highlight .gd { color: #005b82 } /* Generic.Deleted */
+html[data-theme="light"] .highlight .gd { color: #005B82 } /* Generic.Deleted */
html[data-theme="light"] .highlight .ge { font-style: italic } /* Generic.Emph */
-html[data-theme="light"] .highlight .gh { color: #005b82 } /* Generic.Heading */
+html[data-theme="light"] .highlight .gh { color: #005B82 } /* Generic.Heading */
html[data-theme="light"] .highlight .gs { font-weight: bold } /* Generic.Strong */
-html[data-theme="light"] .highlight .gu { color: #005b82 } /* Generic.Subheading */
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-html[data-theme="light"] .highlight .kd { color: #6730c5 } /* Keyword.Declaration */
-html[data-theme="light"] .highlight .kn { color: #6730c5 } /* Keyword.Namespace */
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-html[data-theme="light"] .highlight .m { color: #7f4707 } /* Literal.Number */
-html[data-theme="light"] .highlight .s { color: #00622f } /* Literal.String */
+html[data-theme="light"] .highlight .gu { color: #005B82 } /* Generic.Subheading */
+html[data-theme="light"] .highlight .kc { color: #6730C5 } /* Keyword.Constant */
+html[data-theme="light"] .highlight .kd { color: #6730C5 } /* Keyword.Declaration */
+html[data-theme="light"] .highlight .kn { color: #6730C5 } /* Keyword.Namespace */
+html[data-theme="light"] .highlight .kp { color: #6730C5 } /* Keyword.Pseudo */
+html[data-theme="light"] .highlight .kr { color: #6730C5 } /* Keyword.Reserved */
+html[data-theme="light"] .highlight .kt { color: #7F4707 } /* Keyword.Type */
+html[data-theme="light"] .highlight .ld { color: #7F4707 } /* Literal.Date */
+html[data-theme="light"] .highlight .m { color: #7F4707 } /* Literal.Number */
+html[data-theme="light"] .highlight .s { color: #00622F } /* Literal.String */
html[data-theme="light"] .highlight .na { color: #912583 } /* Name.Attribute */
-html[data-theme="light"] .highlight .nb { color: #7f4707 } /* Name.Builtin */
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+html[data-theme="light"] .highlight .nb { color: #7F4707 } /* Name.Builtin */
+html[data-theme="light"] .highlight .nc { color: #005B82 } /* Name.Class */
+html[data-theme="light"] .highlight .no { color: #005B82 } /* Name.Constant */
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html[data-theme="light"] .highlight .nn { color: #080808 } /* Name.Namespace */
html[data-theme="light"] .highlight .nx { color: #080808 } /* Name.Other */
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-html[data-theme="light"] .highlight .nv { color: #a12236 } /* Name.Variable */
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+html[data-theme="light"] .highlight .py { color: #005B82 } /* Name.Property */
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+html[data-theme="light"] .highlight .mb { color: #7F4707 } /* Literal.Number.Bin */
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+html[data-theme="light"] .highlight .ss { color: #005B82 } /* Literal.String.Symbol */
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html[data-theme="dark"] .highlight pre { line-height: 125%; }
html[data-theme="dark"] .highlight td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
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-html[data-theme="dark"] .highlight .cs { color: #ffd900 } /* Comment.Special */
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+html[data-theme="dark"] .highlight { background: #2b2b2b; color: #F8F8F2 }
+html[data-theme="dark"] .highlight .c { color: #FFD900 } /* Comment */
+html[data-theme="dark"] .highlight .err { color: #FFA07A } /* Error */
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html[data-theme="dark"] .highlight .ge { font-style: italic } /* Generic.Emph */
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index 4db373f..de981a6 100644
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index b269505..3385c12 100644
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index f5682b1..7feb9aa 100644
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@@ -8,7 +8,7 @@
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@@ -8,7 +8,7 @@
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index cd9a73d..c37e02b 100644
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index 93d4ad5..d968e1b 100644
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index 7d0e089..7d9ed09 100644
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How to maintain", "Config", "2. convert functions (specsanalyzer.convert)
", "1. Core functions (specsanalyzer.core)
", "3. image tool functions (specsanalyzer.img_tools)
", "4. io functions (specsanalyzer.io)
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\ No newline at end of file
diff --git a/specsanalyzer/latest/specsanalyzer/config.html b/specsanalyzer/latest/specsanalyzer/config.html
index dc5ce12..04c37df 100644
--- a/specsanalyzer/latest/specsanalyzer/config.html
+++ b/specsanalyzer/latest/specsanalyzer/config.html
@@ -8,7 +8,7 @@
- Config — specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ Config — specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -30,7 +30,7 @@
-
+
@@ -38,7 +38,7 @@
-
+
@@ -47,7 +47,7 @@
@@ -57,7 +57,7 @@
-
+
@@ -119,7 +119,7 @@
- specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -576,7 +576,7 @@ Config#This module contains a config library for loading yaml/json files into dicts
-
-specsanalyzer.config.parse_config(config=None, folder_config=None, user_config=None, system_config=None, default_config='/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/specsanalyzer/config/default.yaml', verbose=True)[source]#
+specsanalyzer.config.parse_config(config=None, folder_config=None, user_config=None, system_config=None, default_config='/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/specsanalyzer/config/default.yaml', verbose=True)[source]#
Load the config dictionary from a file, or pass the provided config dictionary.
The content of the loaded config dictionary is then completed from a set of pre-configured
config files in hierarchical order, by adding missing items. These additional config files
diff --git a/specsanalyzer/latest/specsanalyzer/convert.html b/specsanalyzer/latest/specsanalyzer/convert.html
index 5b734e6..502aa53 100644
--- a/specsanalyzer/latest/specsanalyzer/convert.html
+++ b/specsanalyzer/latest/specsanalyzer/convert.html
@@ -8,7 +8,7 @@
-
2. convert functions (specsanalyzer.convert) — specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ 2. convert functions (specsanalyzer.convert) — specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -30,7 +30,7 @@
-
+
@@ -38,7 +38,7 @@
-
+
@@ -47,7 +47,7 @@
@@ -57,7 +57,7 @@
-
+
@@ -119,7 +119,7 @@
- specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
diff --git a/specsanalyzer/latest/specsanalyzer/core.html b/specsanalyzer/latest/specsanalyzer/core.html
index 6d1244c..92e0f7c 100644
--- a/specsanalyzer/latest/specsanalyzer/core.html
+++ b/specsanalyzer/latest/specsanalyzer/core.html
@@ -8,7 +8,7 @@
- 1. Core functions (specsanalyzer.core) — specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ 1. Core functions (specsanalyzer.core) — specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -30,7 +30,7 @@
-
+
@@ -38,7 +38,7 @@
-
+
@@ -47,7 +47,7 @@
@@ -57,7 +57,7 @@
-
+
@@ -119,7 +119,7 @@
- specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
diff --git a/specsanalyzer/latest/specsanalyzer/img_tools.html b/specsanalyzer/latest/specsanalyzer/img_tools.html
index d0d9533..cbdfb18 100644
--- a/specsanalyzer/latest/specsanalyzer/img_tools.html
+++ b/specsanalyzer/latest/specsanalyzer/img_tools.html
@@ -8,7 +8,7 @@
- 3. image tool functions (specsanalyzer.img_tools) — specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ 3. image tool functions (specsanalyzer.img_tools) — specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -30,7 +30,7 @@
-
+
@@ -38,7 +38,7 @@
-
+
@@ -47,7 +47,7 @@
@@ -57,7 +57,7 @@
-
+
@@ -119,7 +119,7 @@
- specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
diff --git a/specsanalyzer/latest/specsanalyzer/io.html b/specsanalyzer/latest/specsanalyzer/io.html
index 3f6f595..ade9197 100644
--- a/specsanalyzer/latest/specsanalyzer/io.html
+++ b/specsanalyzer/latest/specsanalyzer/io.html
@@ -8,7 +8,7 @@
- 4. io functions (specsanalyzer.io) — specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ 4. io functions (specsanalyzer.io) — specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -30,7 +30,7 @@
-
+
@@ -38,7 +38,7 @@
-
+
@@ -47,7 +47,7 @@
@@ -57,7 +57,7 @@
-
+
@@ -119,7 +119,7 @@
- specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
diff --git a/specsanalyzer/latest/specsscan/core.html b/specsanalyzer/latest/specsscan/core.html
index 23c8efd..52910e0 100644
--- a/specsanalyzer/latest/specsscan/core.html
+++ b/specsanalyzer/latest/specsscan/core.html
@@ -8,7 +8,7 @@
- 1. Core functions (specsscan.core) — specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ 1. Core functions (specsscan.core) — specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -30,7 +30,7 @@
-
+
@@ -38,7 +38,7 @@
-
+
@@ -47,7 +47,7 @@
@@ -57,7 +57,7 @@
-
+
@@ -119,7 +119,7 @@
- specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
diff --git a/specsanalyzer/latest/specsscan/helpers.html b/specsanalyzer/latest/specsscan/helpers.html
index f4a22cd..a408a57 100644
--- a/specsanalyzer/latest/specsscan/helpers.html
+++ b/specsanalyzer/latest/specsscan/helpers.html
@@ -8,7 +8,7 @@
- 2. Helpers — specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ 2. Helpers — specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -30,7 +30,7 @@
-
+
@@ -38,7 +38,7 @@
-
+
@@ -47,7 +47,7 @@
@@ -57,7 +57,7 @@
-
+
@@ -119,7 +119,7 @@
- specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
diff --git a/specsanalyzer/latest/tutorial/1_specsanalyzer_conversion_examples.html b/specsanalyzer/latest/tutorial/1_specsanalyzer_conversion_examples.html
index 33293da..6b2a1f4 100644
--- a/specsanalyzer/latest/tutorial/1_specsanalyzer_conversion_examples.html
+++ b/specsanalyzer/latest/tutorial/1_specsanalyzer_conversion_examples.html
@@ -8,7 +8,7 @@
- Example 1: SpecsAnalyzer conversion — specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ Example 1: SpecsAnalyzer conversion — specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -30,7 +30,7 @@
-
+
@@ -39,7 +39,7 @@
-
+
@@ -50,7 +50,7 @@
@@ -60,7 +60,7 @@
-
+
@@ -122,7 +122,7 @@
- specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -573,9 +573,9 @@ Example 1: SpecsAnalyzer conversion%load_ext autoreload
%autoreload 2
-from specsanalyzer import SpecsAnalyzer
-import matplotlib.pyplot as plt
-import numpy as np
+from specsanalyzer import SpecsAnalyzer
+import matplotlib.pyplot as plt
+import numpy as np
%matplotlib widget
@@ -597,7 +597,7 @@ Image conversion
Configuration loaded from: [/home/runner/work/specsanalyzer/specsanalyzer/docs/tests/data/dataEPFL/config/config.yaml]
-Default config loaded from: [/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/specsanalyzer/config/default.yaml]
+Default config loaded from: [/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/specsanalyzer/config/default.yaml]
convert single image
@@ -657,14 +657,14 @@ Image conversion
-<matplotlib.collections.QuadMesh at 0x7f93b8547010>
+<matplotlib.collections.QuadMesh at 0x7fdfe4554dc0>
-
+
Conversion parameters are stored in the attributes
@@ -734,14 +734,14 @@ Adjusting offsets and angle
-<matplotlib.collections.QuadMesh at 0x7f93b5991c60>
+<matplotlib.collections.QuadMesh at 0x7fdfe3e52b00>
-
+
@@ -761,7 +761,7 @@ Removal of mesh artefact
Configuration loaded from: [/home/runner/work/specsanalyzer/specsanalyzer/docs/tests/data/dataEPFL/config/config_filterON.yaml]
-Default config loaded from: [/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/specsanalyzer/config/default.yaml]
+Default config loaded from: [/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/specsanalyzer/config/default.yaml]
@@ -786,14 +786,14 @@ Removal of mesh artefact
-<matplotlib.collections.QuadMesh at 0x7f93b5db6d40>
+<matplotlib.collections.QuadMesh at 0x7fdfe3e99660>
-
+
Alternatively, one can use the interactive fft tool to optimize the fft peak positions of the grid.
-
+
-
+
-
+
The peak parameters are stored in the config dict which can be passed as kwds to the convert_image function
@@ -855,14 +855,14 @@ Removal of mesh artefact
-<matplotlib.collections.QuadMesh at 0x7f93adc7e080>
+<matplotlib.collections.QuadMesh at 0x7fdfe00b9810>
-
+
@@ -898,14 +898,14 @@ Conversion into spatially resolved modes
-<matplotlib.collections.QuadMesh at 0x7f93adb4a8f0>
+<matplotlib.collections.QuadMesh at 0x7fdfdbf6e4d0>
-
+
@@ -962,7 +962,7 @@ Conversion using conversion_parameters dict
-Default config loaded from: [/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/specsanalyzer/config/default.yaml]
+Default config loaded from: [/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/specsanalyzer/config/default.yaml]
No valid calib2 file found. Please provide the path to the calib2d file
corresponding to your detector in the config, or copy into the config
folder of the package! Without valid calib2d file, calibration parameters
@@ -975,17 +975,17 @@ Conversion using conversion_parameters dict
-<matplotlib.collections.QuadMesh at 0x7f93adbce3b0>
+<matplotlib.collections.QuadMesh at 0x7fdfdbf3f430>
-
+
diff --git a/specsanalyzer/latest/tutorial/2_specsscan_example.html b/specsanalyzer/latest/tutorial/2_specsscan_example.html
index 4c63946..cd63964 100644
--- a/specsanalyzer/latest/tutorial/2_specsscan_example.html
+++ b/specsanalyzer/latest/tutorial/2_specsscan_example.html
@@ -8,7 +8,7 @@
- Example 2: SpecsScan loading — specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ Example 2: SpecsScan loading — specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -30,7 +30,7 @@
-
+
@@ -39,7 +39,7 @@
-
+
@@ -50,7 +50,7 @@
@@ -60,7 +60,7 @@
-
+
@@ -122,7 +122,7 @@
- specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -574,9 +574,9 @@ Example 2: SpecsScan loading%load_ext autoreload
%autoreload 2
-from specsscan import SpecsScan
-import matplotlib.pyplot as plt
-import numpy as np
+from specsscan import SpecsScan
+import matplotlib.pyplot as plt
+import numpy as np
%matplotlib widget
@@ -597,8 +597,8 @@ Example 2: SpecsScan loading
Configuration loaded from: [/home/runner/work/specsanalyzer/specsanalyzer/docs/tests/data/config.yaml]
-Default config loaded from: [/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/specsscan/config/default.yaml]
-Default config loaded from: [/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/specsanalyzer/config/default.yaml]
+Default config loaded from: [/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/specsscan/config/default.yaml]
+Default config loaded from: [/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/specsanalyzer/config/default.yaml]
@@ -621,7 +621,7 @@ Loading data
-
+
@@ -667,14 +667,14 @@ Loading data
-<matplotlib.collections.QuadMesh at 0x7f883acec0a0>
+<matplotlib.collections.QuadMesh at 0x7f9ab13cb1f0>
-
+
@@ -696,7 +696,7 @@ Cropping data
-
+
-
+
-
+
Load the scan again to apply it to all images:
-
+
-
+
-
+
Load the scan again for the new changes to apply to all the images
-
+
@@ -848,14 +848,14 @@ Removal of Mesh Artifact
-<matplotlib.collections.QuadMesh at 0x7f88399c7790>
+<matplotlib.collections.QuadMesh at 0x7f9a5d8b3c40>
-
+
We can e.g. also get a plot along the third dimension, by integrating along the first.
One can also access the conversion result from a class accessor:
@@ -874,14 +874,14 @@ Removal of Mesh Artifact
-<matplotlib.collections.QuadMesh at 0x7f8839437250>
+<matplotlib.collections.QuadMesh at 0x7f9a5d782aa0>
-
+
The metadata associated with the scan is added as an attribute to the xarray
-
+
@@ -949,14 +949,14 @@ Loading with selected iterations
-<matplotlib.collections.QuadMesh at 0x7f883933cfa0>
+<matplotlib.collections.QuadMesh at 0x7f9a5d6a0280>
-
+
Another useful functionality is to load a 3D scan as a function of iterations averaged over the scan parameter (in this case, mirrorX). This is done using the check_scan method
-
+
@@ -1004,14 +1004,14 @@ Loading with selected iterations
-<matplotlib.collections.QuadMesh at 0x7f883975eaa0>
+<matplotlib.collections.QuadMesh at 0x7f9a5d6f7c70>
-
+
@@ -1033,7 +1033,7 @@ Saving#
-
+
@@ -1059,7 +1059,7 @@ Saving#
diff --git a/specsanalyzer/latest/tutorial/3_specsscan_conversion_to_NeXus.html b/specsanalyzer/latest/tutorial/3_specsscan_conversion_to_NeXus.html
index ca3ea75..b4cdd6f 100644
--- a/specsanalyzer/latest/tutorial/3_specsscan_conversion_to_NeXus.html
+++ b/specsanalyzer/latest/tutorial/3_specsscan_conversion_to_NeXus.html
@@ -8,7 +8,7 @@
- Example 3: Export to NeXus — specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ Example 3: Export to NeXus — specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -30,7 +30,7 @@
-
+
@@ -39,7 +39,7 @@
-
+
@@ -50,7 +50,7 @@
@@ -60,7 +60,7 @@
-
+
@@ -122,7 +122,7 @@
- specsanalyzer 0.5.1.dev2+g5d28e05 documentation
+ specsanalyzer 0.5.1.dev10+g0c6ed22 documentation
@@ -574,9 +574,9 @@ Example 3: Export to NeXus%load_ext autoreload
%autoreload 2
-from specsscan import SpecsScan
-import matplotlib.pyplot as plt
-import numpy as np
+from specsscan import SpecsScan
+import matplotlib.pyplot as plt
+import numpy as np
%matplotlib widget
@@ -665,8 +665,8 @@ Example 3: Export to NeXus
User config loaded from: [/home/runner/work/specsanalyzer/specsanalyzer/docs/src/specsscan/config/example_config_FHI.yaml]
-Default config loaded from: [/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/specsscan/config/default.yaml]
-Default config loaded from: [/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/specsanalyzer/config/default.yaml]
+Default config loaded from: [/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/specsscan/config/default.yaml]
+Default config loaded from: [/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/specsanalyzer/config/default.yaml]
The load_scan method loads the scan as an xarray along with the metadata needed for nexus conversion.
@@ -687,7 +687,7 @@ Example 3: Export to NeXus
-
+
@@ -734,14 +734,14 @@ Example 3: Export to NeXus
-<matplotlib.collections.QuadMesh at 0x7f5c6eb1e1a0>
+<matplotlib.collections.QuadMesh at 0x7fe13375ed40>
-
+
The Fermi surface
@@ -759,14 +759,14 @@ Example 3: Export to NeXus
-<matplotlib.collections.QuadMesh at 0x7f5c65f7a650>
+<matplotlib.collections.QuadMesh at 0x7fe1327c60e0>
-
+
Save as nexus file
@@ -573,9 +573,9 @@ Example 4: Sweep Scan loading%load_ext autoreload
%autoreload 2
-from specsscan import SpecsScan
-import matplotlib.pyplot as plt
-import numpy as np
+from specsscan import SpecsScan
+import matplotlib.pyplot as plt
+import numpy as np
%matplotlib widget
@@ -605,8 +605,8 @@ Example 4: Sweep Scan loading
User config loaded from: [/home/runner/work/specsanalyzer/specsanalyzer/docs/src/specsscan/config/example_config_FHI.yaml]
-Default config loaded from: [/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/specsscan/config/default.yaml]
-Default config loaded from: [/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/specsanalyzer/config/default.yaml]
+Default config loaded from: [/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/specsscan/config/default.yaml]
+Default config loaded from: [/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/specsanalyzer/config/default.yaml]
The load_scan method performs the merging of the images and returns the scan as an xarray
@@ -625,7 +625,7 @@ Example 4: Sweep Scan loading
-
+
@@ -674,14 +674,14 @@ Example 4: Sweep Scan loading
-<matplotlib.collections.QuadMesh at 0x7fc9a00eb760>
+<matplotlib.collections.QuadMesh at 0x7ff22834a3b0>
-
+