tomwer 1.3.27__py3-none-any.whl → 1.4.0__py3-none-any.whl

orangecontrib/tomwer/widgets/visualization/SinogramViewerOW.py

@@ -1,31 +1,5 @@
 # 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__ = ["C. Nemoz", "H. Payno"]
-__license__ = "MIT"
-__date__ = "01/08/2018"
+from __future__ import annotations
 
 import logging
 

orangecontrib/tomwer/widgets/visualization/SliceStackOW.py

@@ -1,31 +1,5 @@
 # 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__ = ["C. Nemoz", "H. Payno"]
-__license__ = "MIT"
-__date__ = "04/05/2018"
+from __future__ import annotations
 
 
 import logging
@@ -97,7 +71,7 @@ class SlicesStackOW(widget.OWBaseWidget, openclass=True):
     def addLeafScan(self, scanID, *args, **kwargs):
         if scanID is None:
             return
-        self._viewer.addLeafScan(scanID)
+        self._viewer.addTomoObj(scanID)
 
     def keyPressEvent(self, e):
         # TODO: fixme

tomwer/__init__.py

@@ -1,35 +1,10 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2015-2017 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.
-#
-# ###########################################################################*/
+"""
+tomwer tests
+"""
 
 from __future__ import absolute_import, division, print_function
 
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "27/07/2021"
-
-from tomwer.core.log import logger  # noqa F401
 from tomwer.core.log import processlog  # noqa F401
 from tomwer.version import version as __version  # noqa F401
 

tomwer/__main__.py

@@ -116,7 +116,6 @@ def main():
     This function is referenced in the setup.py file, to create a
     launcher script generated by setuptools.
 
-    :rtype: int
     :returns: The execution status
     """
     _version = tomwer.version.version
@@ -142,7 +141,7 @@ def main():
     launcher.add_command(
         "dark-ref-patch",
         module_name="tomwer.app.patchrawdarkflat",
-        description="patch raw dark and / or flat to an NXTomo entry",
+        description="patch raw dark and / or flat to a NXtomo entry",
         deprecated=True,
         deprecated_reason="improve name",
         deprecated_replacement="patch-raw-dark-flat",
@@ -186,7 +185,7 @@ def main():
     launcher.add_command(
         "nxtomo-editor",
         module_name="tomwer.app.nxtomoeditor",
-        description="Use to edit an NXtomo",
+        description="Use to edit a NXtomo",
     )
     launcher.add_command(
         "ows-to-script",
@@ -196,7 +195,7 @@ def main():
     launcher.add_command(
         "patch-raw-dark-flat",
         module_name="tomwer.app.patchrawdarkflat",
-        description="patch raw dark and / or flat to an NXTomo entry",
+        description="patch raw dark and / or flat to a NXtomo entry",
     )
     launcher.add_command(
         "reduce-dark-flat",
@@ -240,6 +239,11 @@ def main():
     launcher.add_command(
         "test", module_name="tomwer.app.test_", description="Launch tomwer unittest"
     )
+    launcher.add_command(
+        "y-stitching",
+        module_name="tomwer.app.ystitching",
+        description="Launch y-stitcher interface",
+    )
     launcher.add_command(
         "z-stitching",
         module_name="tomwer.app.zstitching",

tomwer/app/__init__.py

@@ -0,0 +1,2 @@
+"""This package contains all the applications that can be launched from 'tomwer'
+"""

tomwer/app/axis.py

@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+"""Application to compute the center of rotation of a scan
+"""
 
 import argparse
 import functools
@@ -20,7 +22,7 @@ from tomwer.core.process.reconstruction.darkref.darkrefs import (
 from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.core.utils.resource import increase_max_number_file
 from tomwer.gui import icons
-from tomwer.gui.reconstruction.axis import AxisWindow
+from tomwer.gui.reconstruction.axis import AxisMainWindow
 from tomwer.gui.utils.splashscreen import getMainSplashScreen
 from tomwer.synctools.axis import QAxisRP
 
@@ -28,10 +30,10 @@ logging.basicConfig(level=logging.WARNING)
 _logger = logging.getLogger(__name__)
 
 
-class _AxisProcessGUI(AxisWindow):
-    def __init__(self, scan, axis_params, backend=None):
+class _AxisProcessGUI(AxisMainWindow):
+    def __init__(self, scan, axis_params, parent=None, backend=None):
         axis_params.frame_width = scan.dim_1
-        super().__init__(axis_params=axis_params, backend=backend)
+        super().__init__(parent=parent, axis_params=axis_params, backend=backend)
         self.hideLockButton()
         self.hideApplyButton()
         self.setScan(scan=scan)
@@ -69,12 +71,11 @@ class _AxisProcessGUI(AxisWindow):
         else:
             position = scan.axis_params.relative_cor_value
             assert isinstance(position, (float, type(None)))
-            frm = "sinogram" if scan.axis_params.use_sinogram else "radio"
-            AxisWindow.setPosition(self, frm=frm, value=position)
+            self.setPosition(relative_value=position)
             return position
 
     def _updatePosition(self, scan):
-        self._widget.setPosition(frm=None, value=scan.axis_params.relative_cor_value)
+        self._widget.setPosition(relative_value=scan.axis_params.relative_cor_value)
 
 
 def main(argv):
@@ -168,9 +169,6 @@ def main(argv):
         _logger.setLevel(logging.DEBUG)
 
     axis_params = QAxisRP()
-    axis_params.use_sinogram = options.use_sinogram
-    if scan.dim_2 is not None:
-        axis_params.sinogram_line = scan.dim_2 // 2
 
     window = _AxisProcessGUI(scan=scan, axis_params=axis_params)
     window.setWindowTitle("axis")

tomwer/app/canvas.py

@@ -1,45 +1,38 @@
+"""Application to define a tomography workflow (also as know as 'ewoks-canvas' or 'orange canvas')
+"""
+
 import logging
 import platform
 import sys
 
 import psutil
-import tomoscan.version
 
-import tomwer.version
 from tomwer.app.canvas_launcher.mainwindow import OMain as QMain
+from tomwer.app.canvas_launcher.utils import get_tomotools_stack_versions
 from tomwer.core.utils.resource import increase_max_number_file
 
 _logger = logging.getLogger(__name__)
 
-try:
-    import nxtomomill.version
-except ImportError:
-    has_nxtomomill = False
-else:
-    has_nxtomomill = True
-try:
-    import nabu
-except ImportError:
-    has_nabu = False
-else:
-    has_nabu = True
-try:
-    import nxtomo.version
-except ImportError:
-    has_nxtomo = False
-else:
-    has_nxtomo = True
-
 
 def print_versions():
-    print(f"tomwer version is {tomwer.version.version}")
-    print(f"tomoscan version is {tomoscan.version.version}")
-    if has_nxtomo:
-        print(f"nxtomo version is {nxtomo.version.version}")
-    if has_nxtomomill:
-        print(f"nxtomomill version is {nxtomomill.version.version}")
-    if has_nabu:
-        print(f"nabu version is {nabu.version}")
+    """Prints the Tomotools packages versions"""
+    print(
+        "\n - ".join(
+            [
+                "Tomotools packages versions:",
+            ]
+            + list(
+                [
+                    f"{soft_name: <11}: {version}"
+                    for soft_name, version in get_tomotools_stack_versions().items()
+                ]
+            )
+        )
+    )
+
+
+def check_free_space():
+    """Check if enough space exists. Else could bring issues on processing"""
     if platform.system() == "Linux":
         try:
             free_home_space = psutil.disk_usage("/home").free
@@ -55,6 +48,7 @@ def print_versions():
 
 def main(argv=None):
     print_versions()
+    check_free_space()
     increase_max_number_file()
     return QMain().run(argv)
 

tomwer/app/canvas_launcher/config.py

@@ -1,48 +1,21 @@
 # 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__ = "14/12/2021"
-
-
-import pkg_resources
-from orangecanvas.application.outputview import (
-    TerminalTextDocument as _TerminalTextDocument,
-)
+from __future__ import annotations
+
 from orangewidget.settings import set_widget_settings_dir_components
 from orangewidget.workflow import config
 from silx.gui import qt
+import logging
 
 import tomwer.version
 from tomwer.gui import icons
 
+from ewoksorange.pkg_meta import iter_entry_points
 from . import environ
 from .splash import getIcon, splash_screen
 from .widgetsscheme import WidgetsScheme
 
+_logger = logging.getLogger(__name__)
+
 
 def version():
     return tomwer.version.version
@@ -79,6 +52,7 @@ class TomwerConfig(config.Config):
 
     @staticmethod
     def splash_screen():
+        """"""
         return splash_screen()
 
     @staticmethod
@@ -103,19 +77,14 @@ class TomwerConfig(config.Config):
         # yields them in unspecified order.
         WIDGETS_ENTRY = "orange.widgets"
 
-        def is_tomwer_extension(entry):
-            return "tomwer" in entry.name.lower()
+        def accept_extension(entry):
+            # safer to ignore some extension like ewoks demo
+            return entry.name.lower() not in ("ewoks demo",)
 
-        all_eps = filter(
-            is_tomwer_extension, pkg_resources.iter_entry_points(WIDGETS_ENTRY)
-        )
-
-        all_eps = sorted(
-            all_eps,
-            key=lambda ep: (
-                0 if ep.dist.project_name.lower() in ("orange3", "tomwer") else 1
-            ),
-        )
+        try:
+            all_eps = filter(accept_extension, iter_entry_points(group=WIDGETS_ENTRY))
+        except Exception as e:
+            _logger.error(f"fail to find add-ons. Error is {e}")
         return iter(all_eps)
 
     @staticmethod
@@ -149,60 +118,3 @@ class TomwerSplashScreen(qt.QSplashScreen):
     def showMessage(self, message, alignment=qt.Qt.AlignLeft, color=qt.Qt.black):
         version = f"tomwer version {tomwer.version.version}"
         super().showMessage(version, qt.Qt.AlignLeft | qt.Qt.AlignBottom, qt.Qt.white)
-
-
-class TerminalTextDocument(_TerminalTextDocument):
-    def __init__(self, parent=None, **kwargs):
-        super().__init__(parent=parent, **kwargs)
-
-    @staticmethod
-    def get_log_level(my_str):
-        if "DEBUG" in my_str:
-            return qt.Qt.darkBlue
-        elif "ERROR" in my_str:
-            return qt.Qt.red
-        elif "WARNING" in my_str:
-            return qt.Qt.magenta
-        elif "CRITICAL" in my_str:
-            return qt.Qt.red
-        elif "Info" in my_str:
-            return qt.Qt.black
-        elif "CRITICAL" in my_str:
-            return qt.Qt.darkYellow
-        elif "PROCESS_STARTED" in my_str:
-            return qt.Qt.black
-        elif "PROCESS_SUCCEED" in my_str:
-            return qt.Qt.darkGreen
-        elif "PROCESS_FAILED" in my_str:
-            return qt.Qt.red
-        elif "PROCESS_ENDED" in my_str:
-            return qt.Qt.black
-        elif "PROCESS_SKIPPED" in my_str:
-            return qt.Qt.magenta
-        else:
-            return None
-
-    def writeWithFormat(self, string: str, charformat) -> None:
-        assert qt.QThread.currentThread() is self.thread()
-        # remove linux reset sequence
-        from tomwer.core.log import logger as tomwer_logger
-
-        for sequence in (
-            tomwer_logger._RESET_SEQ,
-            tomwer_logger._BOLD_SEQ,
-            tomwer_logger._BLACK,
-            tomwer_logger._RED,
-            tomwer_logger._GREEN,
-            tomwer_logger._YELLOW,
-            tomwer_logger._BLUE,
-            tomwer_logger._MAGENTA,
-        ):
-            string = string.replace(sequence, "")
-
-        color = self.get_log_level(string) or qt.Qt.red
-        charformat.setForeground(color)
-
-        # super().writelinesWithFormat(string, charformat)
-        cursor = self.textCursor()
-        cursor.setCharFormat(charformat)
-        cursor.insertText(string)

tomwer/app/canvas_launcher/environ.py

@@ -41,11 +41,12 @@ orangerc.cfg
 
 """
 
+from __future__ import annotations
+
 import configparser
 import os
 import sys
 import sysconfig
-from typing import Optional
 
 import tomwer
 
@@ -75,16 +76,12 @@ def _get_parsed_config():
     return conf
 
 
-def get_path(name: str, default: Optional[str] = None) -> Optional[str]:
+def get_path(name: str, default: str | None = None) -> str | None:
     """
     Get configured path
 
-    Parameters
-    ----------
-    name: str
-        The named config path value
-    default: Optional[str]
-        The default to return if `name` is not defined
+    :param name: The named config path value
+    :param default: The default to return if `name` is not defined
     """
     cfg = _get_parsed_config()
     try: