spell-check all files

.cspell/custom-dictionary.txt

@@ -0,0 +1,150 @@
+# Custom Dictionary Words
+allclose
+ALLUSERSPROFILE
+amperemeter
+analyser
+arange
+archiver
+argwhere
+ARPES
+astype
+autoclass
+automodule
+autoreload
+autosummary
+axhline
+AXISNAME
+axvline
+basepath
+bitshift
+bysource
+calib
+checkscan
+clim
+codemirror
+coeff
+COLLECTIONCOLUMN
+colorbar
+COMPES
+configpath
+Croping
+cropit
+damatrix
+dapolymatrix
+dataconverter
+dataframe
+delaystage
+dtype
+dxda
+dxde
+dyda
+dyde
+Ekin
+electronanalyser
+elems
+endstation
+energydispersion
+eshift
+faddr
+Faradayweg
+fftshift
+filt
+fluence
+fspath
+FWHM
+genindex
+hline
+ifftshift
+IMAGEJ
+imgj
+imread
+imshow
+imutils
+imwrite
+Interp
+ipykernel
+ipympl
+ipython
+ipywidgets
+irfft
+kernelspec
+kwds
+labview
+Laurenz
+lensmodes
+lineh
+linev
+listf
+literalinclude
+loadtxt
+matplotlib
+maxdepth
+mbar
+meshgrid
+modindex
+mpes
+nanos
+nbagg
+nbconvert
+nbformat
+nbsphinx
+ndarray
+ndarrays
+ndim
+ndimage
+ndims
+ndmin
+nesteddict
+nestedentry
+numpy
+nxdl
+Nxpix
+Nxpixels
+Nypixels
+OPCPA
+pcolormesh
+Phoibos
+polyfit
+polyval
+pyenv
+pygments
+pynxtools
+pyplot
+pyproject
+quickstart
+RAWDATA
+Rettig
+rfft
+rrvec
+rtol
+rtype
+scanvector
+specsanalyzer
+Specslab
+specsscan
+stype
+tempa
+tifffile
+tmpdirname
+toctree
+tomlkit
+topfloor
+tqdm
+typehints
+TZCYXS
+undoc
+venv
+vline
+vmax
+vmin
+xarray
+xarrays
+xdata
+xgrid
+Xmpes
+xpos
+Xuser
+ydata
+ygrid
+ypos
+zinner

.gitignore

@@ -138,3 +138,7 @@ dmypy.json
 *.h5
 *.tiff
 *.nxs
+*.pxp
+
+# poetry
+poetry.toml

README.md

@@ -12,7 +12,7 @@ This is the package `specsanalyzer` for conversion and handling of SPECS Phoibos
 
 This package contains two modules:
 `specsanalyzer` is a package to import and convert MCP analyzer images from SPECS Phoibos analyzers into energy and emission angle/physical coordinates.
-`specsscan` is a Python package for loading Specs Phoibos scans accquired with the labview software developed at FHI/EPFL
+`specsscan` is a Python package for loading Specs Phoibos scans acquired with the labview software developed at FHI/EPFL
 
 Tutorials for usage and the API documentation can be found in the [Documentation](https://opencompes.github.io/specsanalyzer/)
 
@@ -47,9 +47,9 @@ python -m ipykernel install --user --name=specs_kernel
 ```
 
 #### Configuration and calib2d file
-The conversion procedures require to set up several configuration parameters in a config file. An example config file is provided as part of the package (see documentation). Configuration files can either be passed to the class constructures, or are read from system-wide or user-defined locations (see documentation).
+The conversion procedures require to set up several configuration parameters in a config file. An example config file is provided as part of the package (see documentation). Configuration files can either be passed to the class constructors, or are read from system-wide or user-defined locations (see documentation).
 
-Most importantly, conversion of analyzer data to energy/angular coordinates requires detector calibration data provided by the manufacturer. The corresponding *.calib2d file (e.g. phoibos150.calbid2d) are provided together with the spectrometer software, and need to be set in the config file.
+Most importantly, conversion of analyzer data to energy/angular coordinates requires detector calibration data provided by the manufacturer. The corresponding *.calib2d file (e.g. phoibos150.calib2d) are provided together with the spectrometer software, and need to be set in the config file.
 
 ### For Contributors
 

cspell.json

@@ -0,0 +1,23 @@
+{
+    "version": "0.2",
+    "ignorePaths": [
+        "./tests/data/*",
+        "*.toml",
+        "Makefile",
+        "*.bat",
+        "*.pxp"
+    ],
+    "dictionaryDefinitions": [
+        {
+            "name": "custom-dictionary",
+            "path": "./.cspell/custom-dictionary.txt",
+            "addWords": true
+        }
+    ],
+    "dictionaries": [
+        "custom-dictionary"
+    ],
+    "words": [],
+    "ignoreWords": [],
+    "import": []
+}

docs/conf.py

@@ -50,8 +50,6 @@ def _get_project_meta():
     "sphinx.ext.autosummary",
     "sphinx.ext.coverage",
     "sphinx_autodoc_typehints",
-    # "bokeh.sphinxext.bokeh_autodoc",
-    # "bokeh.sphinxext.bokeh_plot",
     "nbsphinx",
     "myst_parser",
 ]

docs/specsanalyzer/config.rst

@@ -1,6 +1,6 @@
 Config
 ===================================================
-The config module contains a mechanis to collect configuration parameters from various sources and configuration files, and to combine them in a hierachical manner into a single, consistent configuration dictionary.
+The config module contains a mechanics to collect configuration parameters from various sources and configuration files, and to combine them in a hierarchical manner into a single, consistent configuration dictionary.
 It will load an (optional) provided config file, or alternatively use a passed python dictionary as initial config dictionary, and subsequently look for the following additional config files to load:
 
 * ``folder_config``: A config file of name :file:`specs_config.yaml` in the current working directory. This is mostly intended to pass calibration parameters of the workflow between different notebook instances.

specsanalyzer/config.py

@@ -171,10 +171,10 @@ def load_config(config_path: str) -> dict:
 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 dictionry first.
+    provided dictionary. The overwrite option creates a fully empty dictionary first.
 
     Args:
-        config_dict (dict): The dictionry to save.
+        config_dict (dict): The dictionary to save.
         config_path (str): A string containing the path to the file where to save the dictionary
             to.
         overwrite (bool, optional): Option to overwrite an existing file with the given dictionary.

specsanalyzer/config/default.yaml

@@ -14,5 +14,5 @@ magnification: 4.54
 angle_offset_px: 0
 # offset in pixels along the energy dispersing axis
 energy_offset_px: 0
-# flag controlling the application of a Fourier filter to remove grid artefacts
+# flag controlling the application of a Fourier filter to remove grid artifacts
 apply_fft_filter: false

specsanalyzer/convert.py

@@ -5,7 +5,7 @@
 from scipy.ndimage import map_coordinates
 
 
-def get_damatrix_fromcalib2d(
+def get_damatrix_from_calib2d(
     lens_mode: str,
     kinetic_energy: float,
     pass_energy: float,
@@ -14,7 +14,7 @@ def get_damatrix_fromcalib2d(
 ) -> tuple[float, np.ndarray, float, str, list[str]]:
     """This function estimates the best angular conversion coefficients for the current analyser
     mode, starting from a dictionary containing the specs .calib2d database. A linear interpolation
-    is performed from the tabulated coefficients based on the retardatio ratio value.
+    is performed from the tabulated coefficients based on the retardation ratio value.
 
     Args:
         lens_mode (str): the lens mode string description
@@ -104,7 +104,7 @@ def bisection(array: np.ndarray, value: float) -> int:
     Given an ``array`` , and given a ``value`` , returns an index j such that ``value`` is between
     array[j] and array[j+1]. ``array`` must be monotonic increasing. j=-1 or j=len(array) is
     returned to indicate that ``value`` is out of range below and above respectively.
-    This should mimick the function BinarySearch in igor pro 6
+    This should mimic the function BinarySearch in igor pro 6
 
     Args:
         array (np.ndarray): ordered array
@@ -148,7 +148,7 @@ def second_closest_rr(rrvec: np.ndarray, closest_rr_index: int) -> int:
         int: nearest rr index to calculate the best da coefficients
     """
     if closest_rr_index == (rrvec.size - 1):
-        # we are the edge: the behaviour is to not change the index
+        # we are the edge: the behavior is to not change the index
         second_closest_rr_index = closest_rr_index
     else:
         second_closest_rr_index = closest_rr_index + 1
@@ -160,7 +160,7 @@ def get_rr_da(
     lens_mode: str,
     calib2d_dict: dict,
 ) -> tuple[np.ndarray, np.ndarray]:
-    """Get the retardatio ratios and the da for a certain lens mode from the confugaration
+    """Get the retardation ratios and the da for a certain lens mode from the configuration
     dictionary
 
     Args:
@@ -173,7 +173,7 @@ def get_rr_da(
         ValueError: Raised if no da values are found for the given mode
 
     Returns:
-        tuple[np.ndarray, np.ndarray]: rr vector, matrix of da coeffients
+        tuple[np.ndarray, np.ndarray]: rr vector, matrix of da coefficients
         per row row0 : da1, row1: da3, .. up to da7.
         Non angle resolved lens modes do only posses da1.
     """
@@ -236,26 +236,26 @@ def calculate_polynomial_coef_da(
     pass_energy: float,
     e_shift: np.ndarray,
 ) -> np.ndarray:
-    """Given the da coeffiecients contained in the scanpareters, the program calculates the energy
+    """Given the da coefficients contained in the scan parameters, the program calculates the energy
     range based on the eshift parameter and fits a second order polynomial to the tabulated values.
     The polynomial coefficients are packed in the dapolymatrix array (row0 da1, row1 da3, ..)
-    The function returns a matrix of the fit coeffiecients, given the physical energy scale
+    The function returns a matrix of the fit coefficients, given the physical energy scale
     Each line of the matrix is a set of coefficients for each of the da[i] corrections
 
     Args:
         da_matrix (np.ndarray): the matrix of interpolated da coefficients
-        kinetic_energy (float): photoelectorn kinetic energy
+        kinetic_energy (float): photoelectron kinetic energy
         pass_energy (float): analyser pass energy
         e_shift (np.ndarray): e shift parameter, defining the energy
             range around the center for the polynomial fit of the da coefficients
 
     Returns:
-        np.ndarray: dapolymatrix containg the fit results (row0 da1, row1 da3, ..)
+        np.ndarray: dapolymatrix containing the fit results (row0 da1, row1 da3, ..)
     """
-    # calcualte the energy values for each da, given the eshift
+    # calculate the energy values for each da, given the eshift
     da_energy = e_shift * pass_energy + kinetic_energy * np.ones(e_shift.shape)
 
-    # create the polynomial coeffiecient matrix, each is a second order polynomial
+    # create the polynomial coefficient matrix, each is a second order polynomial
     da_poly_matrix = np.zeros(da_matrix.shape)
 
     for i in range(0, da_matrix.shape[0]):
@@ -279,12 +279,12 @@ def zinner(
     mcp withing the a_inner boundaries
 
     Args:
-        kinetic_energy (flonp.ndarrayat): kinetic energies
+        kinetic_energy (np.ndarray): kinetic energies
         angle (np.ndarray): angles
         da_poly_matrix (np.ndarray): matrix with polynomial coefficients
 
     Returns:
-        np.ndarray: returns the calcualted positions on the mcp, valid for low angles  (< ainner)
+        np.ndarray: returns the calculated positions on the mcp, valid for low angles  (< a_inner)
     """
     out = np.zeros(angle.shape, float)
 
@@ -303,7 +303,7 @@ def zinner_diff(
     da_poly_matrix: np.ndarray,
 ) -> np.ndarray:
     """Auxiliary function for mcp_position_mm, uses kinetic energy and angle starting from the
-    dapolymatrix, to get the zinner_diff coefficient to coorect the electron arrival position on
+    dapolymatrix, to get the zinner_diff coefficient to correct the electron arrival position on
     the mcp outside the a_inner boundaries
 
     Args:
@@ -313,7 +313,7 @@ def zinner_diff(
 
     Returns:
         np.ndarray: zinner_diff the correction for the zinner position on the MCP for high
-        (>ainner) angles.
+        (>a_inner) angles.
     """
 
     out = np.zeros(angle.shape, float)
@@ -349,7 +349,7 @@ def mcp_position_mm(
         np.ndarray: lateral position of photoelectron on the mcp (angular dispersing axis)
     """
 
-    # define two angular regions: within and outsied the a_inner boundaries
+    # define two angular regions: within and outside the a_inner boundaries
     mask = np.less_equal(np.abs(angle), a_inner)
 
     a_inner_vec = np.ones(angle.shape) * a_inner
@@ -513,7 +513,7 @@ def physical_unit_data(
     e_correction_matrix = np.ones(angular_correction_matrix.shape) * e_correction
 
     # flatten the x and y to a 2 x N coordinates array
-    # N = Nxpix x Nypixels
+    # N = Nxpixels x Nypixels
     coords = np.array([angular_correction_matrix.flatten(), e_correction_matrix.flatten()])
 
     # the image is expressed as intensity vs pixels,