tomwer 1.0.3__py3-none-any.whl → 1.1.0__py3-none-any.whl

{tomwer-1.0.3.dist-info → tomwer-1.1.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.36.2)
+Generator: bdist_wheel (0.38.4)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{tomwer-1.0.3.dist-info → tomwer-1.1.0.dist-info}/entry_points.txt

@@ -7,5 +7,11 @@ html-index = orangecontrib.tomwer.widgets:WIDGET_HELP_PATH
 [orange.widgets]
 tomwer = orangecontrib.tomwer.widgets
 
+[orange.widgets.tutorials]
+FLUO = orangecontrib.tomwer.tutorials
+
 [orange3.addon]
 tomwer-add-on = orangecontrib.tomwer
+
+[orangecanvas.examples]
+FLUO = orangecontrib.tomwer.tutorials

orangecontrib/tomwer/setup.py

@@ -1,45 +0,0 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "05/07/2017"
-
-
-from numpy.distutils.misc_util import Configuration
-
-
-def configuration(parent_package="", top_path=None):
-    config = Configuration("tomwer", parent_package, top_path)
-    config.add_subpackage("widgets")
-    config.add_subpackage("test")
-
-    return config
-
-
-if __name__ == "__main__":
-    from numpy.distutils.core import setup
-
-    setup(configuration=configuration)

orangecontrib/tomwer/widgets/setup.py

@@ -1,49 +0,0 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "05/07/2017"
-
-
-from numpy.distutils.misc_util import Configuration
-
-
-def configuration(parent_package="", top_path=None):
-    config = Configuration("widgets", parent_package, top_path)
-    config.add_subpackage("control")
-    config.add_subpackage("edit")
-    config.add_subpackage("other")
-    config.add_subpackage("reconstruction")
-    config.add_subpackage("visualization")
-    config.add_subpackage("test")
-
-    return config
-
-
-if __name__ == "__main__":
-    from numpy.distutils.core import setup
-
-    setup(configuration=configuration)

tomwer/app/process.py

@@ -1,153 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import logging
-import sys
-import argparse
-from ewokscore import load_graph
-from ewoksorange.bindings import owsconvert
-from tomwer.core.scan.scanfactory import ScanFactory
-import tempfile
-import os
-from pprint import pprint
-
-logging.basicConfig(level=logging.WARNING)
-_logger = logging.getLogger(__name__)
-
-
-def exec_scans(name, ewoks_graph, scans=None, darkref_savedir=None):
-    """
-
-    :param ewoks_graph:
-    :param scans: list of scan to execute
-    :param timeout:
-    :return:
-    """
-
-    def launch_():
-        for scan in scans:
-            exec_scan(name=name, ewoks_graph=ewoks_graph, scan=scan, save_dir=save_dir)
-
-    if darkref_savedir is not None:
-        if not os.path.exists(darkref_savedir):
-            os.makedirs(darkref_savedir)
-        launch_()
-    else:
-        with tempfile.TemporaryDirectory() as save_dir:
-            launch_()
-
-
-def exec_scan(name, ewoks_graph, scan, save_dir):
-    # set up workflow
-    if len(ewoks_graph.start_nodes()) == 0:
-        _logger.warning("no start nodes found. Enable to process")
-        return None
-    mess = f"start processing {name} with {str(scan)}"
-    _logger.info(mess)
-
-    # update scan parameter to start node
-    for src_node in ewoks_graph.start_nodes():
-        # provide the dataset to be used and save_dir
-        # save_dir is used to provide dark ref with a directory to store
-        # dark and ref to be copy
-        ewoks_graph.graph.nodes[src_node]["default_inputs"].add(
-            {({"name": "data", "value": scan})}
-        )
-
-    # update node with dark ref
-    import tomwer.core.process.reconstruction.darkref.darkrefscopy
-
-    qual_name = ".".join(
-        [
-            tomwer.core.process.reconstruction.darkref.darkrefscopy.__name__,
-            tomwer.core.process.reconstruction.darkref.darkrefscopy.DarkRefsCopy.__qualname__,
-        ]
-    )
-    for src_node in ewoks_graph.graph.nodes:
-        # provide save_dir to 'darkref' class
-        if ewoks_graph.graph.nodes[src_node]["class"] == qual_name:
-            ewoks_graph.graph.nodes[src_node]["default_inputs"].add(
-                {({"name": "save_dir", "value": save_dir})}
-            )
-        # insure all arguments are provided for each link because the scan object is hidding some
-        # parameters
-        for target_node in ewoks_graph.graph.nodes:
-            if src_node == target_node:
-                continue
-            try:
-                ewoks_graph.graph[src_node][target_node]["all_arguments"] = True
-                del ewoks_graph.graph[src_node][target_node]["arguments"]
-            except KeyError:
-                pass
-
-    print(f" start execution of graph {name} ".center(80, "#"))
-    taskgraph = load_graph(ewoks_graph)
-    pprint(taskgraph.dump())
-    print(f" end execution of graph {name} ".center(80, "#"))
-    ewoks_graph.execute()
-
-
-def main(argv):
-    parser = argparse.ArgumentParser(description=__doc__)
-    parser.add_argument(
-        "workflow_file",
-        help="Path to the .ows file defining the workflow to process with the"
-        "provided scan",
-    )
-    parser.add_argument(
-        "scan_path",
-        help="Path to data to be processes (master file if come from an hdf5 "
-        "acquisition or EDF files folder if come from an EDF acquisition)",
-    )
-    parser.add_argument(
-        "--entry", default=None, help="An entry should be specify for hdf5 files"
-    )
-    parser.add_argument(
-        "--timeout", default=None, help="Timeout for the workflow execution"
-    )
-    parser.add_argument(
-        "--dkref-save-dir",
-        default=None,
-        dest="savedir",
-        help="You can provide a save dir folder for the dark-ref copy task to"
-        "insure persistency between several call of process.",
-    )
-    parser.add_argument(
-        "--debug",
-        dest="debug",
-        action="store_true",
-        default=False,
-        help="Set logging system in debug mode",
-    )
-    options = parser.parse_args(argv[1:])
-    if options.entry is not None:
-        scan = ScanFactory.create_scan_object(
-            options.scan_path, entry=options.entry, accept_bliss_scan=True
-        )
-        scans = (scan,)
-    else:
-        scans = ScanFactory.create_scan_objects(
-            options.scan_path, accept_bliss_scan=True
-        )
-    if len(scans) > 1:
-        _logger.info("More than one scan found. Will process every scans")
-
-    # tune the log level
-    log_level = logging.INFO
-    if options.debug is True:
-        log_level = logging.DEBUG
-
-    for log_ in ("tomwer", "ewoks", "ewoksorange", "ewokscore"):
-        logging.getLogger(log_).setLevel(log_level)
-
-    scheme = owsconvert.ows_to_ewoks(options.workflow_file)
-    exec_scans(
-        name=os.path.basename(options.workflow_file),
-        ewoks_graph=scheme,
-        scans=scans,
-        darkref_savedir=options.savedir,
-    )
-
-
-if __name__ == "__main__":
-    main(sys.argv)

tomwer/core/process/reconstruction/nabu/slurm.py

@@ -1,36 +0,0 @@
-import subprocess
-import logging
-
-_logger = logging.getLogger(__name__)
-
-
-def check_n_gpu():
-    try:
-        from pycuda import driver
-
-        driver.init()
-        n_gpus = driver.Device.count()
-    except Exception as e:
-        raise e
-    else:
-        if n_gpus == 0:
-            raise RuntimeError("No gpu detected to run nabu reconstruction")
-        else:
-            _logger.info(f"{n_gpus} detected by pycuda")
-
-
-def _exec_nabu_on_slurm(conf_file: str, scan_path: str) -> tuple:
-    check_n_gpu()
-
-    NABU_FULL_FIELD_APP_PATH = "nabu.app.reconstruct"
-    # need to be executed in his own context
-    command = " ".join(("python", "-m", NABU_FULL_FIELD_APP_PATH, conf_file))
-    process = subprocess.Popen(
-        command,
-        shell=True,
-        cwd=scan_path,
-        stdout=subprocess.PIPE,
-        stderr=subprocess.PIPE,
-    )
-    res = process.communicate()
-    return res

tomwer/core/process/reconstruction/utils/nabu_slice_exec.py

@@ -1,10 +0,0 @@
-from nabu.pipeline.fullfield.chunked_cuda import CudaChunkedPipeline
-from nabu.pipeline.fullfield.processconfig import ProcessConfig
-
-
-def launch_reconstruction(config_file, slice_index):
-    proc = ProcessConfig(config_file)
-    worker_process = CudaChunkedPipeline(
-        proc, sub_region=(None, None, slice_index, slice_index + 1)
-    )
-    worker_process.process_chunk()

tomwer/core/utils/laminoutils.py

@@ -1,80 +0,0 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2017 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "22/06/2018"
-
-
-import fabio
-import os
-import logging
-
-logger = logging.getLogger(__name__)
-
-
-def getMotorInformationFromEDfFile(_file):
-    """
-
-    :param _file: file to the edf file containing header with information
-    :return: dictionary with motor name as key and motor position as value
-    :rtype: dict
-    """
-    assert type(_file) is str
-    assert _file.endswith(".edf")
-    if not os.path.isfile(_file):
-        warn = "%s is not a valid file. Cannot retrieve motor information" % _file
-        logger.warning(warn)
-        return None
-    else:
-        with fabio.open(_file) as dsc:
-            header = dsc.header
-
-        if "motor_mne" not in header:
-            logger.warning(
-                'key "motor_mne" not found in the file header.'
-                "Cannot retrieve motor information"
-            )
-            return None
-
-        if "motor_pos" not in header:
-            logger.warning(
-                'key "motor_pos" not found in the file header.'
-                "Cannot retrieve motor information"
-            )
-            return None
-
-        motor_mne_lst = header["motor_mne"].split(" ")
-        motor_pos_lst = header["motor_pos"].split(" ")
-        if len(motor_mne_lst) != len(motor_pos_lst):
-            logger.warning(
-                "Incoherent number of motor_mne and motor_pos."
-                "Cannot retrieve motor information"
-            )
-            return None
-        res = {}
-        for mne, pos in zip(motor_mne_lst, motor_pos_lst):
-            res[mne] = pos
-        return res

tomwer/gui/utils/lineselector/lineselection.py

@@ -1,76 +0,0 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "25/09/2017"
-
-import re
-import numpy
-
-SELECTION_PATTERN = re.compile(r"\d?[:]?\d?")
-
-
-def selectionIsValid(selection):
-    """
-    Return true if the given selection as a string is valid
-
-    :return: bool
-    """
-    assert type(selection) is str
-    _selection = selection.replace(" ", "")
-    selections = _selection.split(";")
-    for sel in selections:
-        if not re.match(SELECTION_PATTERN, sel):
-            return False
-    return True
-
-
-def getSelection(projections, selection):
-    """
-
-    :param str selection:
-    :return numpy.ndarray:
-    """
-
-    def evalSelection(projections, sel):
-        assert type(projections) is numpy.ndarray
-        return eval("projections[" + sel + "]")
-
-    assert type(selection) is str
-    if selection == "":
-        return projections
-    _selection = selection.replace(" ", "")
-    selections = _selection.split(";")
-    if len(selections) == 1:
-        return evalSelection(projections, selection)
-    else:
-        res = None
-        for iSel, sel in enumerate(range(len(selections))):
-            if iSel == 0:
-                res = evalSelection(projections, selections[iSel])
-            else:
-                res = numpy.append(res, evalSelection(projections, selections[iSel]))
-        return res

tomwer/setup.py

@@ -1,52 +0,0 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "04/01/2018"
-
-
-from numpy.distutils.misc_util import Configuration
-
-
-def configuration(parent_package="", top_path=None):
-    config = Configuration("tomwer", parent_package, top_path)
-    config.add_subpackage("app")
-    config.add_subpackage("core")
-    config.add_subpackage("gui")
-    config.add_subpackage("io")
-    config.add_subpackage("resources")
-    config.add_subpackage("synctools")
-    config.add_subpackage("test")
-    config.add_subpackage("third_party")
-    config.add_subpackage("web")
-
-    return config
-
-
-if __name__ == "__main__":
-    from numpy.distutils.core import setup
-
-    setup(configuration=configuration)

tomwer/slurm/executor.py

@@ -1,36 +0,0 @@
-from asyncio import Future
-from concurrent.futures import ThreadPoolExecutor
-from typing import Callable
-import time
-from tomwer.slurm.job import SBatchScriptJob, submit_sbatch_job
-
-SUBMISSION_TIMEOUT = 10
-
-_executor = None
-
-
-class Executor(ThreadPoolExecutor):
-    def submit(self, fn: Callable, *args, **kwargs) -> Future:
-        future = super().submit(fn, *args, **kwargs)
-        return future
-
-
-def submit(job: SBatchScriptJob):
-    global _executor
-    if _executor is None:
-        _executor = Executor()
-
-    if not isinstance(job, SBatchScriptJob):
-        raise TypeError(
-            f"job is expected to be an instance of {SBatchScriptJob}. {type(job)} provided"
-        )
-
-    future = _executor.submit(submit_sbatch_job, job)
-    wait_time = 0
-    while job.job_id is None and wait_time < SUBMISSION_TIMEOUT:
-        time.sleep(0.1)
-        wait_time += 0.1
-    future.job_id = job.job_id
-    if job.job_id is None:
-        future.set_exception("Unable to submit job within allocated time")
-    return future