ChessAnalysisPipeline 0.0.14__py3-none-any.whl → 0.0.16__py3-none-any.whl

CHAP/foxden/__init__.py

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+"""This subpackage contains pieces for communication with FOXDEN services.
+"""
+
+from CHAP.foxden.processor import (
+    FoxdenProvenanceProcessor,
+)

CHAP/foxden/processor.py

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+#!/usr/bin/env python
+#-*- coding: utf-8 -*-
+#pylint: disable=
+"""
+File       : processor.py
+Author     : Valentin Kuznetsov <vkuznet AT gmail dot com>
+Description: Processor module for FOXDEN services
+"""
+
+# system modules
+from time import time
+
+# local modules
+from CHAP import Processor
+from CHAP.foxden.writer import FoxdenWriter
+
+
+class FoxdenProvenanceProcessor(Processor):
+    """A Processor to communicate with FOXDEN provenance server."""
+#     def __init__(self):
+#         self.writer = FoxdenWriter()
+
+    def process(self, data, url, dryRun=False, verbose=False):
+        """process data API"""
+
+        t0 = time()
+        self.logger.info(f'Executing "process" with url {url} data {data} dryrun {dryRun}')
+        writer = FoxdenWriter()
+
+#         data = self.writer.write(data, url, dryRun)
+        data = writer.write(data, url, dryRun=dryRun)
+
+        self.logger.info(f'Finished "process" in {time()-t0:.3f} seconds\n')
+
+        return data
+
+
+if __name__ == '__main__':
+    # local modules
+    from CHAP.processor import main
+
+    main()

CHAP/foxden/writer.py

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+"""FOXDE command line writer."""
+
+# system modules
+import os
+
+# Local modules
+from CHAP.writer import main
+
+class FoxdenWriter():
+    """FOXDEN writer writes data to specific FOXDEN service
+    """
+
+    def write(self, data, url, method="POST", headers={}, timeout=10, dryRun=False):
+        """Write the input data as text to a file.
+
+        :param data: input data
+        :type data: list[PipelineData]
+        :param url: url of service
+        :type url: str
+        :param method: HTTP method to use, POST for creation and PUT for update
+        :type method: str
+        :param headers: HTTP headers to use
+        :type headers: dictionary
+        :param timeout: timeout of HTTP request
+        :type timeout: str
+        :param dryRun: dryRun option to verify HTTP workflow
+        :type dryRun: boolean
+        :return: contents of the input data
+        :rtype: object
+        """
+        import requests
+        if 'Content-Type' not in headers:
+            headers['Content-type'] = 'application/json'
+        if 'Accept' not in headers:
+            headers['Accept'] = 'application/json'
+        if dryRun:
+            print("### HTTP writer call", url, headers, data)
+            return []
+        token = ""
+        fname = os.getenv("CHESS_WRITE_TOKEN")
+        if not fname:
+            msg = f'CHESS_WRITE_TOKEN env variable is not set'
+            raise Exception(msg)
+        with open(fname, 'r') as istream:
+            token = istream.read()
+        if token:
+            headers["Authorization"] = f"Bearer {token}"
+        else:
+            msg = f'No valid write token found in CHESS_WRITE_TOKEN env variable'
+            raise Exception(msg)
+
+        # make actual HTTP request to FOXDEN service
+        if method.lower() == 'post':
+            resp = requests.post(url, headers=headers, timeout=timeout, data=data)
+        elif method.lower() == 'put':
+            resp = requests.put(url, headers=headers, timeout=timeout, data=data)
+        else:
+            msg = f"unsupporteed method {method}"
+            raise Exception(msg)
+        data = resp.content
+        return data
+
+
+if __name__ == '__main__':
+    main()

CHAP/giwaxs/__init__.py

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+"""This subpackage contains `PipelineItems` unique to GIWAXS data
+processing workflows.
+"""
+# from CHAP.giwaxs.reader import
+# from CHAP.giwaxs.processor import
+# from CHAP.giwaxs.writer import
+
+from CHAP.giwaxs.processor import GiwaxsConversionProcessor

CHAP/giwaxs/models.py

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+# System modules
+from functools import cache
+import os
+from pathlib import PosixPath
+from typing import (
+    Optional,
+)
+
+# Third party modules
+import numpy as np
+from pydantic import (
+    BaseModel,
+    DirectoryPath,
+    FilePath,
+    conint,
+    conlist,
+    constr,
+    field_validator,
+    model_validator,
+)
+
+# Local modules
+from CHAP.common.models.map import MapConfig
+
+
+class Detector(BaseModel):
+    """Detector class to represent a single detector used in the
+    experiment.
+
+    :param prefix: Prefix of the detector in the SPEC file.
+    :type prefix: str
+    :param poni_file: Path to the poni file.
+    :type poni_file: str
+    """
+    prefix: constr(strip_whitespace=True, min_length=1)
+    poni_file: FilePath
+
+    @field_validator('poni_file')
+    @classmethod
+    def validate_poni_file(cls, poni_file):
+        """Validate the poni file by checking if it's a valid PONI
+        file.
+
+        :param poni_file: Path to the poni file.
+        :type poni_file: str
+        :raises ValueError: If poni_file is not a valid PONI file.
+        :returns: Absolute path to the poni file.
+        :rtype: str
+        """
+        # Third party modules
+        from pyFAI import load
+
+        poni_file = os.path.abspath(poni_file)
+        try:
+            load(poni_file)
+        except Exception as exc:
+            raise ValueError(f'{poni_file} is not a valid PONI file') from exc
+        return poni_file
+
+
+class GiwaxsConversionConfig(BaseModel):
+    """Class representing metadata required to locate GIWAXS image
+    files for a single scan to convert to q_par/q_perp coordinates.
+
+    :ivar detectors: List of detector configurations.
+    :type detectors: list[Detector]
+    :ivar scan_step_indices: Optional scan step indices to convert.
+        If not specified, all images will be converted.
+    :type scan_step_indices: Union(int, list[int], str), optional
+    :ivar save_raw_data: Save the raw data in the NeXus output,
+        default to `False`.
+    :type save_raw_data: bool, optional
+    """
+    detectors: conlist(item_type=Detector, min_length=1)
+    scan_step_indices: Optional[
+        conlist(item_type=conint(ge=0), min_length=1)] = None
+    save_raw_data: Optional[bool] = False
+
+    @field_validator('scan_step_indices', mode='before')
+    @classmethod
+    def validate_scan_step_indices(cls, scan_step_indices):
+        """Validate the specified list of scan step indices.
+
+        :param scan_step_indices: List of scan numbers.
+        :type scan_step_indices: list of int
+        :raises ValueError: If a specified scan number is not found in
+            the SPEC file.
+        :return: List of scan numbers.
+        :rtype: list of int
+        """
+        if isinstance(scan_step_indices, int):
+            scan_step_indices = [scan_step_indices]
+        if isinstance(scan_step_indices, str):
+            # Local modules
+            from CHAP.utils.general import string_to_list
+
+            scan_step_indices = string_to_list(scan_step_indices)
+
+        return scan_step_indices
+