crispy 0.8.0__py3-none-any.whl

crispy/__init__.py

@@ -0,0 +1,22 @@
+###################################################################
+# Copyright (c) 2016-2024 European Synchrotron Radiation Facility #
+#                                                                 #
+# Author: Marius Retegan                                          #
+#                                                                 #
+# This work is licensed under the terms of the MIT license.       #
+# For further information, see https://github.com/mretegan/crispy #
+###################################################################
+"""This is the Crispy package."""
+
+__version__ = "0.8.0"
+import os
+import sys
+
+version = __version__
+
+
+# https://stackoverflow.com/questions/7674790/bundling-data-files-with-pyinstaller-onefile
+def resourceAbsolutePath(relativePath):
+    """Get the absolute path to a resource. Works for development and for PyInstaller."""
+    basePath = getattr(sys, "_MEIPASS", os.path.dirname(os.path.abspath(__file__)))
+    return os.path.join(basePath, relativePath)

crispy/__main__.py

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+###################################################################
+# Copyright (c) 2016-2024 European Synchrotron Radiation Facility #
+#                                                                 #
+# Author: Marius Retegan                                          #
+#                                                                 #
+# This work is licensed under the terms of the MIT license.       #
+# For further information, see https://github.com/mretegan/crispy #
+###################################################################
+"""This module is the entry point to the application."""
+
+import json
+import logging
+import numpy as np
+import os
+import socket
+import sys
+import warnings
+from urllib.error import URLError
+from urllib.request import Request, urlopen
+
+from silx.gui.qt import (
+    QAction,
+    QApplication,
+    QByteArray,
+    QDialog,
+    QIcon,
+    QLocale,
+    QMainWindow,
+    QPixmap,
+    QPlainTextEdit,
+    QPoint,
+    QSize,
+    Qt,
+    QThread,
+    QProcess,
+    QFileDialog,
+    pyqtSignal,
+)
+
+from crispy import resourceAbsolutePath, version
+from crispy.config import Config
+from crispy.loggers import StatusBarHandler, setUpLoggers
+from crispy.plot import MainPlotWidget  # noqa: F401
+from crispy.quanty.main import DockWidget
+from crispy.uic import loadUi
+from crispy.utils import fixedFont
+
+logger = logging.getLogger("crispy.main")
+warnings.filterwarnings("ignore", category=UserWarning)
+
+settings = Config().read()
+
+
+class MainWindow(QMainWindow):
+    def __init__(self, parent=None):
+        super().__init__(parent=parent)
+
+        uiPath = os.path.join("uis", "main.ui")
+        loadUi(resourceAbsolutePath(uiPath), baseinstance=self)
+
+        self.setWindowTitle("Crispy")
+
+        # Set the icon.
+        iconPath = os.path.join("crispy.png")
+        self.setWindowIcon(QIcon(resourceAbsolutePath(iconPath)))
+
+        # Setup the logger widget.
+        self.loggerWidget.setFont(fixedFont())
+        self.loggerWidget.setLineWrapMode(QPlainTextEdit.NoWrap)
+
+        # Setup the about dialog.
+        self.aboutDialog = AboutDialog(parent=self)
+
+        # Instantiate the Quanty dock widget.
+        self.quantyDockWidget = DockWidget(parent=self)
+        self.quantyDockWidget.setVisible(True)
+        self.addDockWidget(Qt.RightDockWidgetArea, self.quantyDockWidget)
+
+        # Compose the menu.
+        menu = self.menuBar().addMenu("Quanty")
+        menu.addAction(self.quantyDockWidget.preferencesAction)
+        menu.addSeparator()
+        menu.addAction(self.quantyDockWidget.saveInputAction)
+        menu.addAction(self.quantyDockWidget.saveInputAsAction)
+        menu.addSeparator()
+        menu.addAction(self.quantyDockWidget.showHideAction)
+
+        menu = self.menuBar().addMenu("Tools")
+        self.loadExternalDataAction = QAction(
+            "Load External Data", self, triggered=self.loadExternalData
+        )
+        menu.addAction(self.loadExternalDataAction)
+
+        self.runJupyterLabAction = QAction(
+            "Start Jupyter Lab", self, triggered=self.runJupyterLab
+        )
+        menu.addAction(self.runJupyterLabAction)
+
+        menu = self.menuBar().addMenu("Help")
+        self.openAboutDialogAction = QAction(
+            "About Crispy", self, triggered=self.openAboutDialog
+        )
+        menu.addAction(self.openAboutDialogAction)
+
+        # Register a handler to display messages in the status bar.
+        logger = logging.getLogger("crispy")
+        handler = StatusBarHandler()
+        logger.addHandler(handler)
+        # If I don't set the level here, the handler will also display debug
+        # messages, even though the level is set to INFO in the __init__ method.
+        handler.setLevel(logging.INFO)
+        handler.bridge.logUpdated.connect(self.updateStatusBar)
+
+    def updateStatusBar(self, message):
+        self.statusBar().showMessage(message, 3000)
+
+    def showEvent(self, event):
+        self.loadSettings()
+        super().showEvent(event)
+
+    def closeEvent(self, event):
+        self.saveSettings()
+        super().closeEvent(event)
+
+    def loadSettings(self):
+        settings.beginGroup("MainWindow")
+
+        state = settings.value("State")
+        if state is not None:
+            self.restoreState(QByteArray(state))
+
+        size = settings.value("Size")
+        if size is not None:
+            self.resize(QSize(size))
+
+        pos = settings.value("Position")
+        if pos is not None:
+            self.move(QPoint(pos))
+
+        splitter = settings.value("Splitter")
+        if splitter is not None:
+            sizes = [int(size) for size in splitter]
+        else:
+            sizes = [6, 1]
+        self.splitter.setSizes(sizes)
+        settings.endGroup()
+
+    def saveSettings(self):
+        settings.beginGroup("MainWindow")
+        settings.setValue("State", self.saveState())
+        settings.setValue("Size", self.size())
+        settings.setValue("Position", self.pos())
+        settings.setValue("Splitter", self.splitter.sizes())
+        settings.endGroup()
+
+        settings.sync()
+
+    def openAboutDialog(self):
+        self.aboutDialog.exec()
+
+    def loadExternalData(self):
+        dialog = QFileDialog()
+        path, _ = dialog.getOpenFileName(self, "Select File")
+
+        if path:
+            try:
+                x, y = np.loadtxt(path, unpack=True)
+            except ValueError:
+                logger.error(f"Failed to load data from {path}")
+                return
+
+            name = os.path.splitext(os.path.basename(path))[0]
+            self.quantyDockWidget.addExternalData(name, x, y)
+
+    def runJupyterLab(self):
+        process = QProcess()
+        process.setProgram("jupyter-lab")
+        process.setArguments([f"--notebook-dir={os.path.expanduser('~')}"])
+        process.startDetached()
+
+
+class CheckUpdateThread(QThread):
+    updateAvailable = pyqtSignal()
+
+    @staticmethod
+    def _getSiteVersion():
+        URL = "http://www.esrf.eu/computing/scientific/crispy/version.json"
+
+        request = Request(URL)
+        request.add_header("Cache-Control", "max-age=0")
+
+        try:
+            response = urlopen(request, timeout=5)
+        except (URLError, socket.timeout):
+            return None
+
+        try:
+            data = json.loads(response.read().decode("utf-8"))
+        except Exception:
+            return None
+
+        return data["version"]
+
+    def run(self):
+        # TODO: The implementation is not ideal. The run() method of the parent
+        # class is not called.
+        # Wait a few seconds to avoid too much work at startup.
+        seconds = 1
+        self.sleep(seconds)
+        siteVersion = self._getSiteVersion()
+
+        if siteVersion is not None and version < siteVersion:
+            self.updateAvailable.emit()
+        else:
+            logger.info("There are no updates.")
+
+
+class UpdateAvailableDialog(QDialog):
+    def __init__(self, parent):
+        super().__init__(parent)
+
+        uiPath = os.path.join("uis", "update.ui")
+        loadUi(resourceAbsolutePath(uiPath), baseinstance=self)
+
+
+class AboutDialog(QDialog):
+    def __init__(self, parent):
+        super().__init__(parent)
+
+        uiPath = os.path.join("uis", "about.ui")
+        loadUi(resourceAbsolutePath(uiPath), baseinstance=self)
+
+        self.nameLabel.setText(f"Crispy {version}")
+
+        self.updateCheckBox.stateChanged.connect(self.updateCheckBoxStateChanged)
+        self.updateCheckBox.setChecked(settings.value("CheckForUpdates", type=bool))
+
+        iconPath = resourceAbsolutePath(os.path.join("icons", "crispy.svg"))
+        self.iconLabel.setPixmap(QPixmap(iconPath))
+
+        if settings.value("CheckForUpdates", type=bool):
+            self.runUpdateCheck()
+
+    def updateCheckBoxStateChanged(self):
+        updateCheck = self.updateCheckBox.isChecked()
+        settings.setValue("CheckForUpdates", updateCheck)
+        if updateCheck:
+            self.runUpdateCheck()
+
+    def runUpdateCheck(self):
+        thread = CheckUpdateThread(self)
+        thread.start()
+        thread.updateAvailable.connect(self.informAboutAvailableUpdate)
+
+    def informAboutAvailableUpdate(self):
+        updateAvailableDialog = UpdateAvailableDialog(self.parent())
+        updateAvailableDialog.show()
+
+
+def main():
+    app = QApplication([])
+
+    # This must be done after the application is instantiated.
+    locale = QLocale(QLocale.C)
+    locale.setNumberOptions(QLocale.OmitGroupSeparator)
+    QLocale.setDefault(locale)
+
+    config = Config()
+    config.prune()
+
+    setUpLoggers()
+
+    logger.info("Starting the application.")
+    window = MainWindow()
+    window.show()
+    logger.info("Ready.")
+
+    sys.exit(app.exec())
+
+
+if __name__ == "__main__":
+    main()

crispy/broaden.py

@@ -0,0 +1,112 @@
+###################################################################
+# Copyright (c) 2016-2024 European Synchrotron Radiation Facility #
+#                                                                 #
+# Author: Marius Retegan                                          #
+#                                                                 #
+# This work is licensed under the terms of the MIT license.       #
+# For further information, see https://github.com/mretegan/crispy #
+###################################################################
+"""The module implements fast FFT broadening."""
+
+from math import ceil
+
+import numpy as np
+
+
+def gaussian_kernel1d(sigma=None, truncate=4):
+    size = ceil(2 * truncate * sigma + 1)
+    if size % 2 == 0:
+        size = size + 1
+    x = np.arange(size)
+    mu = np.median(x)
+    # The prefactor 1 / (sigma * np.sqrt(2 * np.pi)) drops in the normalization.
+    kernel = np.exp(-0.5 * ((x - mu) ** 2 / sigma**2))
+    if kernel.sum() < np.finfo(float).eps:
+        raise Exception(
+            f"The kernel can't be normalized, because its sum is {kernel.sum():.1e}."
+        )
+    kernel /= kernel.sum()
+    return kernel
+
+
+def gaussian_kernel2d(sigma=None, truncate=(4, 4)):
+    if len(sigma) != 2 or len(truncate) != 2:
+        raise ValueError(
+            "Sigma and the truncation parameter don't have the required dimensions."
+        )
+    kernel_x = gaussian_kernel1d(sigma[0], truncate[0])
+    kernel_y = gaussian_kernel1d(sigma[1], truncate[1])
+    kernel = np.outer(kernel_y, kernel_x)
+    return kernel
+
+
+def convolve_fft(array, kernel):
+    """Convolve an array with a kernel using FFT.
+
+    Implementation based on the convolve_fft function from astropy:
+    https://github.com/astropy/astropy/blob/main/astropy/convolution/convolve.py
+    """
+    array = np.asarray(array, dtype=complex)
+    kernel = np.asarray(kernel, dtype=complex)
+
+    if array.ndim != kernel.ndim:
+        raise ValueError("Image and kernel must have same number of dimensions")
+
+    new_shape = np.array(array.shape) + np.array(kernel.shape)
+
+    array_slices = []
+    kernel_slices = []
+    for new_dimsize, array_dimsize, kernel_dimsize in zip(
+        new_shape, array.shape, kernel.shape
+    ):
+        center = new_dimsize - (new_dimsize + 1) // 2
+        array_slices += [
+            slice(center - array_dimsize // 2, center + (array_dimsize + 1) // 2)
+        ]
+        kernel_slices += [
+            slice(center - kernel_dimsize // 2, center + (kernel_dimsize + 1) // 2)
+        ]
+
+    array_slices = tuple(array_slices)
+    kernel_slices = tuple(kernel_slices)
+
+    if not np.all(new_shape == array.shape):
+        big_array = np.zeros(new_shape, dtype=complex)
+        big_array[array_slices] = array
+    else:
+        big_array = array
+
+    if not np.all(new_shape == kernel.shape):
+        big_kernel = np.zeros(new_shape, dtype=complex)
+        big_kernel[kernel_slices] = kernel
+    else:
+        big_kernel = kernel
+
+    array_fft = np.fft.fftn(big_array)
+    kernel_fft = np.fft.fftn(np.fft.ifftshift(big_kernel))
+
+    rifft = np.fft.ifftn(array_fft * kernel_fft)
+
+    return rifft[array_slices].real
+
+
+def broaden(array, fwhm=None, kind="gaussian"):
+    if fwhm is None:
+        return array
+
+    fwhm = np.array(fwhm)
+    if (fwhm <= 0).any():
+        return array
+
+    kernel = None
+    if kind == "gaussian":
+        sigma = fwhm / (2 * np.sqrt(2 * np.log(2)))
+        if fwhm.size == 1:
+            kernel = gaussian_kernel1d(sigma)
+        elif fwhm.size == 2:
+            kernel = gaussian_kernel2d(sigma)
+
+    if kernel is None:
+        return array
+
+    return convolve_fft(array, kernel)

crispy/config.py

@@ -0,0 +1,109 @@
+###################################################################
+# Copyright (c) 2016-2024 European Synchrotron Radiation Facility #
+#                                                                 #
+# Author: Marius Retegan                                          #
+#                                                                 #
+# This work is licensed under the terms of the MIT license.       #
+# For further information, see https://github.com/mretegan/crispy #
+###################################################################
+"""The modules provides a class to deal with the configuration."""
+
+import logging
+import os
+import shutil
+import sys
+
+from packaging.version import parse
+from silx.gui.qt import QSettings, QStandardPaths
+
+from crispy import resourceAbsolutePath, version
+
+logger = logging.getLogger(__name__)
+
+
+class Config:
+    @property
+    def name(self):
+        return "Crispy" if sys.platform == "win32" else "crispy"
+
+    @property
+    def path(self):
+        return os.path.split(self.read().fileName())[0]
+
+    def read(self):
+        return QSettings(
+            QSettings.IniFormat, QSettings.UserScope, self.name, "settings"
+        )
+
+    def default(self):
+        """Set default settings."""
+        settings = self.read()
+        settings.clear()
+
+        logger.debug("Setting the default values.")
+
+        settings.beginGroup("Quanty")
+        settings.setValue("Path", self.findQuanty())
+        settings.setValue("Verbosity", "0x0000")
+        settings.setValue("DenseBorder", "2000")
+        settings.setValue("ShiftSpectra", True)
+        settings.setValue("RemoveFiles", True)
+        settings.endGroup()
+
+        settings.setValue("CheckForUpdates", True)
+        settings.setValue("CurrentPath", os.path.expanduser("~"))
+        settings.setValue("Version", version)
+
+        settings.sync()
+
+    def prune(self):
+        """Remove previous config files."""
+
+        root = QStandardPaths.standardLocations(QStandardPaths.GenericConfigLocation)[0]
+        path = os.path.join(root, self.name)
+        if os.path.exists(path):
+            shutil.rmtree(path, ignore_errors=True)
+
+        versionFromSettings = self.read().value("Version")
+        if versionFromSettings is None or parse(versionFromSettings) != parse(version):
+            path, _ = os.path.split(self.read().fileName())
+            shutil.rmtree(path, ignore_errors=True)
+            self.default()
+
+    @staticmethod
+    def findQuanty():
+        executable = "Quanty"
+        if sys.platform == "win32":
+            executable = f"{executable}.exe"
+            localPath = resourceAbsolutePath(os.path.join("quanty", "bin", "win32"))
+        elif sys.platform == "darwin":
+            localPath = resourceAbsolutePath(os.path.join("quanty", "bin", "darwin"))
+        elif sys.platform == "linux":
+            localPath = resourceAbsolutePath(os.path.join("quanty", "bin", "linux"))
+        else:
+            localPath = None
+
+        if localPath is not None:
+            localPath = QStandardPaths.findExecutable(executable, [localPath])
+
+        envPath = QStandardPaths.findExecutable(executable)
+        # Check if Quanty is in the paths defined in the $PATH.
+        if envPath:
+            path = envPath
+        # Check if Quanty is bundled with Crispy.
+        elif localPath is not None:
+            path = localPath
+        else:
+            path = None
+
+        if path is None:
+            logger.debug(
+                "Could not find the Quanty executable."
+                'Please set it up using the "Preferences" dialog.'
+            )
+
+        return path
+
+    def setQuantyPath(self, path):
+        self.read().setValue("Quanty/Path", path)
+        self.read().sync()

crispy/icons/clipboard.svg

@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE svg  PUBLIC '-//W3C//DTD SVG 1.1//EN'  'http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd'>
+<svg clip-rule="evenodd" fill-rule="evenodd" stroke-linecap="round" stroke-linejoin="round" stroke-miterlimit="1.5" version="1.1" viewBox="0 0 2048 2048" xml:space="preserve" xmlns="http://www.w3.org/2000/svg">
+    <g transform="matrix(.25009 0 0 .25009 -43.054 -43.069)">
+        <path d="m6465.7 1334.6h-1221.7c0-538.92-438.44-977.36-977.36-977.36s-977.36 438.44-977.36 977.36h-1221.7c-404.84 0-733.02 328.18-733.02 733.02v5375.5c0 404.84 328.18 733.02 733.02 733.02h4398.1c404.84 0 733.02-328.18 733.02-733.02v-5375.5c0-404.84-328.18-733.02-733.02-733.02h0.02zm-91.63 6108.5h-4214.8c-50.26 0-91.62-41.36-91.62-91.63v-5192.2c0-50.26 41.36-91.62 91.62-91.62h641.39v549.76c0 101.2 82.06 183.26 183.25 183.26h2565.6c101.2 0 183.25-82.06 183.25-183.26v-549.76h641.39c50.27 0 91.63 41.36 91.63 91.62v5192.2c0 50.27-41.36 91.63-91.63 91.63h-0.08zm-2107.4-6475c202.42 0 366.51 164.09 366.51 366.51s-164.09 366.51-366.51 366.51-366.51-164.09-366.51-366.51 164.09-366.51 366.51-366.51" fill-rule="nonzero"/>
+        <path d="m2831.1 4196.1h2871.2" fill="none" stroke="#000" stroke-width="625px"/>
+        <path d="m2831.1 5761.8h2871.2" fill="none" stroke="#000" stroke-width="625px"/>
+    </g>
+</svg>

crispy/icons/cog.svg

@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<svg version="1.1" viewBox="0 0 2048 2048" xmlns="http://www.w3.org/2000/svg">
+ <path d="m1741.4 1157.4 161.94 93.476c18.495 10.674 27.079 32.748 20.744 53.143-42.066 135.44-113.89 257.8-207.82 359.43a45.661 45.661 0 0 1-56.362 8.5652l-161.82-93.461a727.99 727.99 0 0 1-230.88 133.49v186.89a45.638 45.638 0 0 1-35.633 44.528c-132.83 29.83-275.5 31.373-415.03 0.038-20.862-4.6854-35.731-23.165-35.731-44.547v-186.9a727.91 727.91 0 0 1-230.88-133.49l-161.82 93.461a45.661 45.661 0 0 1-56.362-8.5652c-93.928-101.63-165.75-223.99-207.82-359.43-6.3346-20.391 2.2496-42.465 20.744-53.143l161.94-93.488a735.22 735.22 0 0 1 0-266.76l-161.94-93.476c-18.495-10.674-27.079-32.748-20.744-53.143 42.066-135.44 113.89-257.8 207.82-359.43a45.661 45.661 0 0 1 56.362-8.5652l161.82 93.461a727.99 727.99 0 0 1 230.88-133.49v-186.9a45.638 45.638 0 0 1 35.633-44.528c132.83-29.83 275.5-31.373 415.03-0.038 20.862 4.6854 35.731 23.165 35.731 44.547v186.9a727.91 727.91 0 0 1 230.88 133.49l161.82-93.461a45.661 45.661 0 0 1 56.362 8.5652c93.928 101.63 165.75 223.99 207.82 359.43 6.3346 20.391-2.2496 42.465-20.744 53.143l-161.94 93.476a735.24 735.24 0 0 1 0 266.76zm-413.39-133.38c0-167.63-136.37-304-304-304s-304 136.37-304 304 136.37 304 304 304 304-136.37 304-304z" stroke-width="3.8"/>
+</svg>

crispy/icons/crispy.svg

@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE svg  PUBLIC '-//W3C//DTD SVG 1.1//EN'  'http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd'>
+<svg clip-rule="evenodd" fill-rule="evenodd" version="1.1" viewBox="0 0 1007 1007" xml:space="preserve" xmlns="http://www.w3.org/2000/svg">
+    <g transform="translate(-1367.2 -1940.2)">
+        <g transform="scale(4.1667)">
+            <g transform="translate(-.69718 165.43)">
+                <path d="m548.6 421c0 54.672-44.32 98.991-98.992 98.991-54.671 0-98.991-44.319-98.991-98.991 0-54.671 44.32-98.991 98.991-98.991 54.672 0 98.992 44.32 98.992 98.991" fill="#1f78b4" fill-rule="nonzero"/>
+            </g>
+        </g>
+        <g transform="scale(4.1667)">
+            <g transform="matrix(0 -1.2379 -1.2379 -0 970.07 1143)">
+                <ellipse cx="449.61" cy="421" rx="77.588" ry="77.589" fill="none" stroke="#a6cee3" stroke-width="9.69px"/>
+            </g>
+        </g>
+        <g transform="scale(4.1667)">
+            <g transform="matrix(.42909 .42909 -.42909 .42909 450.8 -507.87)">
+                <path d="m1273.1 1171.7c-58.34 0-105.63 47.29-105.63 105.63 0 58.29 47.33 105.62 105.63 105.62 58.33 0 105.63-47.29 105.63-105.62" fill="none" stroke="#2fa037" stroke-linecap="round" stroke-linejoin="round" stroke-miterlimit="1.5" stroke-width="16.48px"/>
+            </g>
+        </g>
+        <g transform="scale(4.1667)">
+            <g transform="matrix(.30605 .30605 -.30605 .30605 450.58 -194.15)">
+                <path d="m1273.1 1171.7c-58.34 0-105.63 47.29-105.63 105.63 0 58.29 47.33 105.62 105.63 105.62 58.33 0 105.63-47.29 105.63-105.62" fill="none" stroke="#b3d388" stroke-linecap="round" stroke-linejoin="round" stroke-miterlimit="1.5" stroke-width="23.1px"/>
+            </g>
+        </g>
+        <g transform="scale(4.1667)">
+            <g transform="matrix(.42567 0 0 .42567 -253.21 87.72)">
+                <circle cx="1662.6" cy="1278.6" r="24.667" fill="#b3d388"/>
+            </g>
+        </g>
+        <g transform="scale(4.1667)">
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+                <circle cx="1662.6" cy="1278.6" r="24.667" fill="#2fa037"/>
+            </g>
+        </g>
+    </g>
+</svg>

crispy/icons/folder-open.svg

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+</svg>

crispy/icons/play.svg

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+</svg>

crispy/icons/save.svg

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+<?xml version="1.0" encoding="UTF-8"?>
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+</svg>

crispy/icons/stop.svg

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+</svg>

crispy/icons/trash.svg

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+<?xml version="1.0" encoding="UTF-8"?>
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