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+[[package]] +name = "tzlocal" +version = "4.3" +description = "tzinfo object for the local timezone" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"}, - {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"}, + {file = "tzlocal-4.3-py3-none-any.whl", hash = "sha256:b44c4388f3d34f25862cfbb387578a4d70fec417649da694a132f628a23367e2"}, + {file = "tzlocal-4.3.tar.gz", hash = "sha256:3f21d09e1b2aa9f2dacca12da240ca37de3ba5237a93addfd6d593afe9073355"}, ] +[package.dependencies] +"backports.zoneinfo" = {version = "*", markers = "python_version < \"3.9\""} +pytz-deprecation-shim = "*" +tzdata = {version = "*", markers = "platform_system == \"Windows\""} + +[package.extras] +devenv = ["black", "check-manifest", "flake8", "pyroma", "pytest (>=4.3)", "pytest-cov", "pytest-mock (>=3.3)", "zest.releaser"] + [[package]] name = "uncertainties" version = "3.1.7" @@ -5456,7 +5592,7 @@ name = "uri-template" version = "1.3.0" description = "RFC 6570 URI Template Processor" category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "uri-template-1.3.0.tar.gz", hash = "sha256:0e00f8eb65e18c7de20d595a14336e9f337ead580c70934141624b6d1ffdacc7"}, @@ -5483,14 +5619,14 @@ six = "*" [[package]] name = "urllib3" -version = "2.0.4" +version = "2.0.6" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "urllib3-2.0.4-py3-none-any.whl", hash = "sha256:de7df1803967d2c2a98e4b11bb7d6bd9210474c46e8a0401514e3a42a75ebde4"}, - {file = "urllib3-2.0.4.tar.gz", hash = "sha256:8d22f86aae8ef5e410d4f539fde9ce6b2113a001bb4d189e0aed70642d602b11"}, + {file = "urllib3-2.0.6-py3-none-any.whl", hash = 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+5652,7 @@ name = "webcolors" version = "1.13" description = "A library for working with the color formats defined by HTML and CSS." category = "main" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "webcolors-1.13-py3-none-any.whl", hash = "sha256:29bc7e8752c0a1bd4a1f03c14d6e6a72e93d82193738fa860cbff59d0fcc11bf"}, @@ -5532,7 +5668,7 @@ name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" category = "main" -optional = false +optional = true python-versions = "*" files = [ {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"}, @@ -5541,36 +5677,33 @@ files = [ [[package]] name = "websocket-client" -version = "1.6.1" +version = "1.6.3" description = "WebSocket client for Python with low level API options" category = "main" -optional = false -python-versions = ">=3.7" +optional = true +python-versions = ">=3.8" files = [ - {file = "websocket-client-1.6.1.tar.gz", hash = "sha256:c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd"}, - {file = "websocket_client-1.6.1-py3-none-any.whl", hash = "sha256:f1f9f2ad5291f0225a49efad77abf9e700b6fef553900623060dad6e26503b9d"}, + {file = "websocket-client-1.6.3.tar.gz", hash = "sha256:3aad25d31284266bcfcfd1fd8a743f63282305a364b8d0948a43bd606acc652f"}, + {file = "websocket_client-1.6.3-py3-none-any.whl", hash = "sha256:6cfc30d051ebabb73a5fa246efdcc14c8fbebbd0330f8984ac3bb6d9edd2ad03"}, ] [package.extras] -docs = ["Sphinx (>=3.4)", "sphinx-rtd-theme (>=0.5)"] +docs = ["Sphinx (>=6.0)", "sphinx-rtd-theme (>=1.1.0)"] optional = ["python-socks", "wsaccel"] test = ["websockets"] [[package]] name = "widgetsnbextension" -version = "3.6.5" -description = "IPython HTML widgets for Jupyter" +version = "4.0.9" +description = "Jupyter interactive widgets for Jupyter Notebook" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.7" files = [ - {file = "widgetsnbextension-3.6.5-py2.py3-none-any.whl", hash = "sha256:a5ae5e8ac0a85b9c527bee8ecb60b3e4b9ce499ed2900c9335b4d94e59f2e086"}, - {file = "widgetsnbextension-3.6.5.tar.gz", hash = "sha256:601352aa4df7b15717fc57ab59fd9f2795003e53c477dca0d53171c4ee933b35"}, + {file = "widgetsnbextension-4.0.9-py3-none-any.whl", hash = "sha256:91452ca8445beb805792f206e560c1769284267a30ceb1cec9f5bcc887d15175"}, + {file = "widgetsnbextension-4.0.9.tar.gz", hash = "sha256:3c1f5e46dc1166dfd40a42d685e6a51396fd34ff878742a3e47c6f0cc4a2a385"}, ] -[package.dependencies] -notebook = ">=4.4.1" - [[package]] name = "xarray" version = "0.20.2" @@ -5597,23 +5730,24 @@ viz = ["matplotlib", "nc-time-axis", "seaborn"] [[package]] name = "zarr" -version = "2.16.0" +version = "2.16.1" description = "An implementation of chunked, compressed, N-dimensional arrays for Python" category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "zarr-2.16.0-py3-none-any.whl", hash = "sha256:6cf9e6e4c58b9233262e024394e68921a438a6af5a7428bd6bdb1e4e8d05b69a"}, - {file = "zarr-2.16.0.tar.gz", hash = "sha256:84e36b695bda0ecea52af9861271984cb22a5c864679907b7b9ba3f79b684f7e"}, + {file = "zarr-2.16.1-py3-none-any.whl", hash = "sha256:de4882433ccb5b42cc1ec9872b95e64ca3a13581424666b28ed265ad76c7056f"}, + {file = "zarr-2.16.1.tar.gz", hash = "sha256:4276cf4b4a653431042cd53ff2282bc4d292a6842411e88529964504fb073286"}, ] [package.dependencies] asciitree = "*" fasteners = "*" numcodecs = ">=0.10.0" -numpy = ">=1.20" +numpy = ">=1.20,<1.21.0 || >1.21.0" [package.extras] +docs = ["numcodecs[msgpack]", "numpydoc", "pydata-sphinx-theme", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx-issues", "sphinx-rtd-theme"] jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"] [[package]] @@ -5629,25 +5763,25 @@ files = [ [[package]] name = "zipp" -version = "3.16.2" +version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"}, - {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"}, + {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, + {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [extras] -docs = ["sphinx", "sphinx-rtd-theme", "tomlkit", "sphinx-autodoc-typehints"] -notebook = ["jupyter", "ipykernel"] +docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-rtd-theme", "tomlkit"] +notebook = ["ipykernel", "jupyter"] [metadata] lock-version = "2.0" python-versions = ">=3.8,<3.11" -content-hash = "9477cb466f2fd33e340ce705e8106180d638586696ce74be39ac2a4232ff6c70" +content-hash = "d0ffb3199374ca1e88d3f03cc425b5a0cfcc60abac23b1dcd4fdd4f66267492a" diff --git a/pyproject.toml b/pyproject.toml index e362ea2a..45b9b400 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,8 +11,8 @@ dask = ">=2021.12.0, <2023.0.0" fastdtw = "^0.3.4" fastparquet = "^0.8.0" h5py = "^3.6.0" -ipympl = "^0.9.1" -ipywidgets = "^7.7.1" +ipympl = ">=0.9.1" +ipywidgets = ">=7.7.1" lmfit = "^1.0.3" matplotlib = "^3.5.1" natsort = "^8.1.0" @@ -21,7 +21,7 @@ numpy = ">=1.18,<1.22" opencv-python = "<=4.8.0.74" pandas = "^1.4.1" psutil = "^5.9.0" -pynxtools = "^0.0.2" +pynxtools = ">=0.0.2" pyyaml = "^6.0.0" scipy = "^1.8.0" symmetrize = "^0.5.5" diff --git a/sed/calibrator/momentum.py b/sed/calibrator/momentum.py index 9ee81eb6..7fb585de 100644 --- a/sed/calibrator/momentum.py +++ b/sed/calibrator/momentum.py @@ -99,6 +99,8 @@ def __init__( self.vvdist: float = np.nan self.rdeform_field: np.ndarray = None self.cdeform_field: np.ndarray = None + self.rdeform_field_bkp: np.ndarray = None + self.cdeform_field_bkp: np.ndarray = None self.inverse_dfield: np.ndarray = None self.dfield_updated: bool = False self.transformations: Dict[Any, Any] = {} @@ -108,12 +110,8 @@ def __init__( self.x_column = self._config["dataframe"]["x_column"] self.y_column = self._config["dataframe"]["y_column"] - self.corrected_x_column = self._config["dataframe"][ - "corrected_x_column" - ] - self.corrected_y_column = self._config["dataframe"][ - "corrected_y_column" - ] + self.corrected_x_column = self._config["dataframe"]["corrected_x_column"] + self.corrected_y_column = self._config["dataframe"]["corrected_y_column"] self.kx_column = self._config["dataframe"]["kx_column"] self.ky_column = self._config["dataframe"]["ky_column"] @@ -613,6 +611,7 @@ def spline_warp_estimate( use_center: bool = None, fixed_center: bool = True, interp_order: int = 1, + verbose: bool = True, **kwds, ) -> np.ndarray: """Estimate the spline deformation field using thin plate spline registration. @@ -629,6 +628,8 @@ def spline_warp_estimate( interp_order (int, optional): Order of interpolation (see ``scipy.ndimage.map_coordinates()``). Defaults to 1. + verbose (bool, optional): Option to report the used landmarks for correction. + Defaults to True. **kwds: keyword arguments: - **landmarks**: (list/array): Landmark positions (row, column) used @@ -712,6 +713,10 @@ def spline_warp_estimate( splinewarp[1], ) + # save backup copies to reset transformations + self.rdeform_field_bkp = self.rdeform_field + self.cdeform_field_bkp = self.cdeform_field + self.correction["applied"] = True self.correction["pouter"] = self.pouter_ord self.correction["pcent"] = np.asarray(self.pcent) @@ -723,6 +728,12 @@ def spline_warp_estimate( if self.slice is not None: self.slice_corrected = corrected_image + if verbose: + print("Calulated thin spline correction based on the following landmarks:") + print(f"pouter: {self.pouter}") + if use_center: + print(f"pcent: {self.pcent}") + return corrected_image def apply_correction( @@ -966,6 +977,8 @@ def pose_adjustment( ytrans: float = 0, angle: float = 0, apply: bool = False, + reset: bool = True, + verbose: bool = True, ): """Interactive panel to adjust transformations that are applied to the image. Applies first a scaling, next a x/y translation, and last a rotation around @@ -983,12 +996,23 @@ def pose_adjustment( apply (bool, optional): Option to directly apply the provided transformations. Defaults to False. + reset (bool, optional): + Option to reset the correction before transformation. Defaults to True. + verbose (bool, optional): + Option to report the performed transformations. Defaults to True. """ matplotlib.use("module://ipympl.backend_nbagg") source_image = self.slice_corrected transformed_image = source_image + if reset: + if self.rdeform_field_bkp is not None and self.cdeform_field_bkp is not None: + self.rdeform_field = self.rdeform_field_bkp + self.cdeform_field = self.cdeform_field_bkp + else: + self.reset_deformation() + fig, ax = plt.subplots(1, 1) img = ax.imshow(transformed_image.T, origin="lower", cmap="terrain_r") center = self._config["momentum"]["center_pixel"] @@ -1050,6 +1074,7 @@ def update(scale: float, xtrans: float, ytrans: float, angle: float): step=1, ) angle_slider = ipw.FloatSlider(value=angle, min=-180, max=180, step=1) + results_box = ipw.Output() ipw.interact( update, scale=scale_slider, @@ -1066,6 +1091,9 @@ def apply_func(apply: bool): # pylint: disable=unused-argument yscale=self.transformations["scale"], keep=True, ) + if verbose: + with results_box: + print(f"Applied scaling with scale={self.transformations['scale']}.") if ( self.transformations.get("xtrans", 0) != 0 or self.transformations.get("ytrans", 0) != 0 @@ -1076,6 +1104,12 @@ def apply_func(apply: bool): # pylint: disable=unused-argument ytrans=self.transformations["ytrans"], keep=True, ) + if verbose: + with results_box: + print( + f"Applied translation with (xtrans={self.transformations['xtrans']},", + f"ytrans={self.transformations['ytrans']}).", + ) if self.transformations.get("angle", 0) != 0: self.coordinate_transform( transform_type="rotation", @@ -1083,6 +1117,11 @@ def apply_func(apply: bool): # pylint: disable=unused-argument center=center, keep=True, ) + if verbose: + with results_box: + print(f"Applied rotation with angle={self.transformations['angle']}.") + + display(results_box) img.set_data(self.slice_transformed.T) axmin = np.min(self.slice_transformed, axis=(0, 1)) diff --git a/sed/core/processor.py b/sed/core/processor.py index d95a7e5d..9069215c 100644 --- a/sed/core/processor.py +++ b/sed/core/processor.py @@ -512,6 +512,7 @@ def pose_adjustment( angle: float = 0, apply: bool = False, use_correction: bool = True, + reset: bool = True, ): """3. step of the distortion correction workflow: Generate an interactive panel to adjust affine transformations that are applied to the image. Applies first @@ -531,6 +532,8 @@ def pose_adjustment( transformations. Defaults to False. use_correction (bool, option): Whether to use the spline warp correction or not. Defaults to True. + reset (bool, optional): + Option to reset the correction before transformation. Defaults to True. """ # Generate homomorphy as default if no distortion correction has been applied if self.mc.slice_corrected is None: @@ -544,7 +547,7 @@ def pose_adjustment( self.mc.reset_deformation() if self.mc.cdeform_field is None or self.mc.rdeform_field is None: - # Generate default distortion correction + # Generate distortion correction from config values self.mc.add_features() self.mc.spline_warp_estimate() @@ -554,6 +557,7 @@ def pose_adjustment( ytrans=ytrans, angle=angle, apply=apply, + reset=reset, ) # 5. Apply the momentum correction to the dataframe @@ -1483,6 +1487,8 @@ def save( config["nexus"]["definition"] - **input_files**: A list of input files to pass to the reader. Defaults to config["nexus"]["input_files"] + - **eln_data**: An electronic-lab-notebook file in '.yaml' format + to add to the list of files to pass to the reader. """ if self._binned is None: raise NameError("Need to bin data first!") @@ -1520,6 +1526,9 @@ def save( if isinstance(input_files, str): input_files = [input_files] + if "eln_data" in kwds: + input_files.append(kwds.pop("eln_data")) + to_nexus( data=self._binned, faddr=faddr, diff --git a/sed/loader/mpes/loader.py b/sed/loader/mpes/loader.py index d1126a73..965abe91 100644 --- a/sed/loader/mpes/loader.py +++ b/sed/loader/mpes/loader.py @@ -4,6 +4,7 @@ @author: L. Rettig """ import datetime +import glob import json import os import urllib @@ -19,6 +20,7 @@ import h5py import numpy as np import scipy.interpolate as sint +from natsort import natsorted from sed.loader.base.loader import BaseLoader @@ -362,14 +364,30 @@ def read_dataframe( Tuple[ddf.DataFrame, dict]: Dask dataframe and metadata read from specified files. """ - # pylint: disable=duplicate-code - super().read_dataframe( - files=files, - folders=folders, - runs=runs, - ftype=ftype, - metadata=metadata, - ) + # if runs is provided, try to locate the respective files relative to the provided folder. + if runs is not None: # pylint: disable=duplicate-code + files = [] + if isinstance(runs, (str, int)): + runs = [runs] + for run in runs: + files.extend( + self.get_files_from_run_id(run_id=run, folders=folders, extension=ftype), + ) + self.runs = list(runs) + super().read_dataframe( + files=files, + ftype=ftype, + metadata=metadata, + ) + else: + # pylint: disable=duplicate-code + super().read_dataframe( + files=files, + folders=folders, + runs=runs, + ftype=ftype, + metadata=metadata, + ) hdf5_groupnames = kwds.pop( "hdf5_groupnames", @@ -425,7 +443,7 @@ def get_files_from_run_id( self, run_id: str, folders: Union[str, Sequence[str]] = None, - extension: str = None, + extension: str = "h5", **kwds, ) -> List[str]: """Locate the files for a given run identifier. @@ -433,14 +451,37 @@ def get_files_from_run_id( Args: run_id (str): The run identifier to locate. folders (Union[str, Sequence[str]], optional): The directory(ies) where the raw - data is located. Defaults to None. + data is located. Defaults to config["core"]["base_folder"] extension (str, optional): The file extension. Defaults to "h5". kwds: Keyword arguments Return: - str: Path to the location of run data. + List[str]: List of file path strings to the location of run data. """ - raise NotImplementedError + if folders is None: + folders = self._config["core"]["paths"]["data_raw_dir"] + + if isinstance(folders, str): + folders = [folders] + + files: List[str] = [] + for folder in folders: + run_files = natsorted( + glob.glob( + folder + "/**/Scan" + str(run_id).zfill(4) + "_*." + extension, + recursive=True, + ), + ) + files.extend(run_files) + + # Check if any files are found + if not files: + raise FileNotFoundError( + f"No files found for run {run_id} in directory {str(folders)}", + ) + + # Return the list of found files + return files def gather_metadata( self, diff --git a/tests/data/loader/mpes/config.yaml b/tests/data/loader/mpes/config.yaml index e901b4d3..877c531a 100644 --- a/tests/data/loader/mpes/config.yaml +++ b/tests/data/loader/mpes/config.yaml @@ -1 +1,3 @@ -test: +core: + paths: + data_raw_dir: "tests/data/loader/mpes/" diff --git a/tests/loader/test_loaders.py b/tests/loader/test_loaders.py index 1ab85cff..1d744088 100644 --- a/tests/loader/test_loaders.py +++ b/tests/loader/test_loaders.py @@ -22,7 +22,7 @@ test_data_dir = os.path.join(package_dir, "..", "tests", "data") read_types = ["one_file", "files", "one_folder", "folders", "one_run", "runs"] -runs = {"generic": None, "mpes": None, "flash": ["43878", "43878"]} +runs = {"generic": None, "mpes": ["30", "50"], "flash": ["43878", "43878"]} def get_loader_name_from_loader_object(loader: BaseLoader) -> str: