OASYS2-XRayServer 1.0.0__tar.gz

oasys2_xrayserver-1.0.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2025, Organization managing the OASYS project
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

oasys2_xrayserver-1.0.0/MANIFEST.in

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+recursive-include orangecontrib *.pyx
+recursive-include orangecontrib *.py
+
+recursive-include orangecontrib/xrayserver/widgets *.png *.svg *.ico *.jpg *.bmp
+
+include README.md

oasys2_xrayserver-1.0.0/OASYS2_XRayServer.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: OASYS2-XRayServer
+Version: 1.0.0
+Summary: X-Ray Server: Sergey Stepanov's X-Ray Server on OASYS 2
+Home-page: https://github.com/oasys-kit/OASYS2-XRayServer
+Download-URL: https://github.com/oasys-kit/OASYS2-XRayServer
+Author: Luca Rebuffi
+Author-email: lrebuffi@anl.gov
+License: GPLv3
+Keywords: X-ray optics,simulator,oasys2
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: X11 Applications :: Qt
+Classifier: Environment :: Console
+Classifier: Environment :: Plugins
+Classifier: Programming Language :: Python :: 3
+Classifier: Intended Audience :: Science/Research
+License-File: LICENSE
+Requires-Dist: oasys2>=0.0.1
+Requires-Dist: PyQtWebEngine>=5.15.7
+Requires-Dist: dabax
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: download-url
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: summary
+
+#XRayServer
+
+This is the project for XRayServer (Sergey Stepanov's X-Ray Server) under OASYS 2

oasys2_xrayserver-1.0.0/OASYS2_XRayServer.egg-info/SOURCES.txt

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+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+setup.py
+OASYS2_XRayServer.egg-info/PKG-INFO
+OASYS2_XRayServer.egg-info/SOURCES.txt
+OASYS2_XRayServer.egg-info/dependency_links.txt
+OASYS2_XRayServer.egg-info/entry_points.txt
+OASYS2_XRayServer.egg-info/not-zip-safe
+OASYS2_XRayServer.egg-info/requires.txt
+OASYS2_XRayServer.egg-info/top_level.txt
+orangecontrib/__init__.py
+orangecontrib/xrayserver/__init__.py
+orangecontrib/xrayserver/util/__init__.py
+orangecontrib/xrayserver/util/list_utility.py
+orangecontrib/xrayserver/util/xrayserver_util.py
+orangecontrib/xrayserver/widgets/__init__.py
+orangecontrib/xrayserver/widgets/gui/__init__.py
+orangecontrib/xrayserver/widgets/gui/ow_xrayserver_widget.py
+orangecontrib/xrayserver/widgets/xrayserver/__init__.py
+orangecontrib/xrayserver/widgets/xrayserver/ow_gid_sl.py
+orangecontrib/xrayserver/widgets/xrayserver/ow_ter_sl.py
+orangecontrib/xrayserver/widgets/xrayserver/ow_x0h.py
+orangecontrib/xrayserver/widgets/xrayserver/ow_x0p.py
+orangecontrib/xrayserver/widgets/xrayserver/icons/gidsl.png
+orangecontrib/xrayserver/widgets/xrayserver/icons/list.png
+orangecontrib/xrayserver/widgets/xrayserver/icons/no_standing_waves_result.png
+orangecontrib/xrayserver/widgets/xrayserver/icons/tersl.png
+orangecontrib/xrayserver/widgets/xrayserver/icons/x0h.png
+orangecontrib/xrayserver/widgets/xrayserver/icons/x0p.png
+orangecontrib/xrayserver/widgets/xrayserver/icons/xrayserver.png

oasys2_xrayserver-1.0.0/OASYS2_XRayServer.egg-info/dependency_links.txt

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+

oasys2_xrayserver-1.0.0/OASYS2_XRayServer.egg-info/entry_points.txt

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+[oasys2.addons]
+xrayserver = orangecontrib.xrayserver
+
+[oasys2.widgets]
+X-Ray Server = orangecontrib.xrayserver.widgets.xrayserver

oasys2_xrayserver-1.0.0/OASYS2_XRayServer.egg-info/not-zip-safe

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+

oasys2_xrayserver-1.0.0/OASYS2_XRayServer.egg-info/requires.txt

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+oasys2>=0.0.1
+PyQtWebEngine>=5.15.7
+dabax

oasys2_xrayserver-1.0.0/OASYS2_XRayServer.egg-info/top_level.txt

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+orangecontrib

oasys2_xrayserver-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: OASYS2-XRayServer
+Version: 1.0.0
+Summary: X-Ray Server: Sergey Stepanov's X-Ray Server on OASYS 2
+Home-page: https://github.com/oasys-kit/OASYS2-XRayServer
+Download-URL: https://github.com/oasys-kit/OASYS2-XRayServer
+Author: Luca Rebuffi
+Author-email: lrebuffi@anl.gov
+License: GPLv3
+Keywords: X-ray optics,simulator,oasys2
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: X11 Applications :: Qt
+Classifier: Environment :: Console
+Classifier: Environment :: Plugins
+Classifier: Programming Language :: Python :: 3
+Classifier: Intended Audience :: Science/Research
+License-File: LICENSE
+Requires-Dist: oasys2>=0.0.1
+Requires-Dist: PyQtWebEngine>=5.15.7
+Requires-Dist: dabax
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: download-url
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: summary
+
+#XRayServer
+
+This is the project for XRayServer (Sergey Stepanov's X-Ray Server) under OASYS 2

oasys2_xrayserver-1.0.0/README.md

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+#XRayServer
+
+This is the project for XRayServer (Sergey Stepanov's X-Ray Server) under OASYS 2

oasys2_xrayserver-1.0.0/orangecontrib/xrayserver/util/list_utility.py

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+from orangecontrib.xrayserver.util.xrayserver_util import HttpManager
+
+APPLICATION = "/cgi/www_dbli.exe"
+
+class ListUtility:
+    @classmethod
+    def get_list(cls, x0hdb=""):
+
+        parameters = {}
+        parameters.update({"x0hdb" : x0hdb})
+        parameters.update({"textout" : "1" })
+        parameters.update({"namesonly" : "1"})
+
+        try:
+            response = HttpManager.send_xray_server_request_GET(APPLICATION, parameters)
+
+            list = response.split('\n')
+            return [x.strip() for x in list[1:len(list)-1]]
+
+        except Exception as e:
+            return []
+
+
+    @classmethod
+    def get_help(cls, x0hdb=""):
+
+        parameters = {}
+        parameters.update({"x0hdb" : x0hdb})
+
+        try:
+            return HttpManager.send_xray_server_request_GET(APPLICATION, parameters)
+
+        except Exception as e:
+            return ""

oasys2_xrayserver-1.0.0/orangecontrib/xrayserver/util/xrayserver_util.py

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+import os
+
+from orangewidget import gui
+
+from PyQt5 import QtWidgets
+from PyQt5.QtWebEngineWidgets import QWebEngineView as QWebView
+
+import matplotlib
+import urllib
+
+from dabax.dabax_xraylib import DabaxXraylib
+
+dabax = DabaxXraylib()
+
+XRAY_SERVER_URL = "https://x-server.gmca.aps.anl.gov"
+TMP_FILE = "xrayserver_tmp.txt"
+
+import ssl
+ssl._create_default_https_context = ssl._create_unverified_context
+
+class HttpManager():
+
+    @classmethod
+    def send_xray_server_request_GET(cls, application, parameters):
+        # this code prevent the real X-Ray Server to see Oasys as a bot.
+        opener = urllib.request.build_opener()
+        opener.addheaders = [('User-Agent', 'Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1941.0 Safari/537.36')]
+        urllib.request.install_opener(opener)
+        urllib.request.urlretrieve(XRAY_SERVER_URL + application + "?" + urllib.parse.urlencode(parameters), TMP_FILE)
+
+        with open(TMP_FILE) as f:
+            content = f.read()
+            f.close()
+
+        try: os.remove(TMP_FILE)
+        except: pass
+
+        return content
+
+    @classmethod
+    def send_xray_server_direct_request(cls, url, decode=True):
+        resp = urllib.request.urlopen(url=XRAY_SERVER_URL+url)
+
+        if decode: return resp.read().decode('ascii')
+        else:      return resp.read()
+
+class XRayServerPhysics:
+    @classmethod
+    def getMaterialDensity(cls, material_formula):
+        if material_formula is None: return 0.0
+        if str(material_formula.strip()) == "": return 0.0
+
+        try:
+            compoundData = dabax.CompoundParser(material_formula)
+
+            if compoundData["nElements"] == 1:
+                return dabax.ElementDensity(compoundData["Elements"][0])
+            else:
+                return 0.0
+        except:
+            return 0.0
+
+class XRayServerGui:
+
+    @classmethod
+    def format_scientific(cls, lineedit):
+        lineedit.setText("{:.2e}".format(float(lineedit.text().replace("+", ""))))
+
+
+    @classmethod
+    def combobox_text(cls, widget, master, value, box=None, label=None, labelWidth=None,
+             orientation='vertical', items=(), callback=None,
+             sendSelectedValue=False, selectedValue=None,
+             **misc):
+
+        combo = gui.comboBox(widget, master, value, box=box, label=label, labelWidth=labelWidth, orientation=orientation,
+                             items=items, callback=callback, sendSelectedValue=sendSelectedValue, **misc)
+        try:
+            combo.setCurrentIndex(items.index(selectedValue))
+        except:
+            pass
+
+        return combo
+
+class XRayServerPlot:
+
+    @classmethod
+    def plot_histo(cls, plot_window, x, y, title, xtitle, ytitle):
+        matplotlib.rcParams['axes.formatter.useoffset']='False'
+
+        plot_window.addCurve(x, y, title, symbol='', color='blue', replace=True) #'+', '^', ','
+        if not xtitle is None: plot_window.setGraphXLabel(xtitle)
+        if not ytitle is None: plot_window.setGraphYLabel(ytitle)
+        if not title is None: plot_window.setGraphTitle(title)
+
+        if min(y) < 0:
+            plot_window.setGraphYLimits(1.01*min(y), max(y)*1.01)
+        else:
+            plot_window.setGraphYLimits(min(y), max(y)*1.01)
+        plot_window.replot()
+
+class ShowHtmlDialog(QtWidgets.QDialog):
+
+    def __init__(self, title, html_text, width=650, height=400, parent=None):
+        QtWidgets.QDialog.__init__(self, parent)
+        self.setModal(True)
+        self.setWindowTitle(title)
+        layout = QtWidgets.QVBoxLayout(self)
+
+        web_view = QWebView(self)
+        web_view.setHtml(html_text)
+
+        text_area = QtWidgets.QScrollArea(self)
+        text_area.setWidget(web_view)
+        text_area.setWidgetResizable(True)
+        text_area.setFixedHeight(height)
+        text_area.setFixedWidth(width)
+
+        bbox = QtWidgets.QDialogButtonBox(QtWidgets.QDialogButtonBox.Ok)
+
+        bbox.accepted.connect(self.accept)
+        layout.addWidget(text_area)
+        layout.addWidget(bbox)
+
+    @classmethod
+    def show_html(cls, title, html_text, width=650, height=400, parent=None):
+        dialog = ShowHtmlDialog(title, html_text, width, height, parent)
+        dialog.show()

oasys2_xrayserver-1.0.0/orangecontrib/xrayserver/widgets/gui/ow_xrayserver_widget.py

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+import numpy
+
+from oasys2.widget.widget import OWWidget, OWAction
+
+from PyQt5.QtWidgets import QApplication, QSizePolicy
+from PyQt5.QtCore import QRect
+
+import oasys2.widget.gui as oasysgui
+from oasys2.canvas.util.canvas_util import ShowTextDialog
+
+from orangecontrib.xrayserver.util.xrayserver_util import HttpManager, XRayServerPlot
+from orangecontrib.xrayserver.util.list_utility import ListUtility
+
+class XrayServerWidget(OWWidget):
+    plot_canvas = []
+
+    MAX_WIDTH = 1400
+    MAX_HEIGHT = 700
+
+    def __init__(self):
+        super().__init__()
+
+        self.runaction = OWAction("Submit Request", self)
+        self.runaction.triggered.connect(self.submit)
+        self.addAction(self.runaction)
+
+        geom = QApplication.desktop().availableGeometry()
+        self.setGeometry(QRect(round(geom.width()*0.05),
+                               round(geom.height()*0.05),
+                               round(min(geom.width()*0.98, self.MAX_WIDTH)),
+                               round(min(geom.height()*0.95, self.MAX_HEIGHT))))
+
+        self.setMaximumHeight(self.geometry().height())
+        self.setMaximumWidth(self.geometry().width())
+
+        self.left_side.setSizePolicy(QSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.MinimumExpanding))
+        self.left_side.setMaximumWidth(self.getLeftPartWidth())
+        self.left_side.updateGeometry()
+
+
+    def getLeftPartWidth(self):
+        return 515
+
+    def get_lines(self):
+        return ListUtility.get_list("waves")
+
+    def help_lines(self):
+        ShowTextDialog.show_text("Help Waves", ListUtility.get_help("waves"), width=350, parent=self)
+
+    def get_crystals(self):
+        return ListUtility.get_list("crystals")
+
+    def help_crystals(self):
+        ShowTextDialog.show_text("Help Crystals", ListUtility.get_help("crystals"), parent=self)
+
+    def get_others(self):
+        return ListUtility.get_list("amorphous+atoms")
+
+    def help_others(self):
+        ShowTextDialog.show_text("Help Others", ListUtility.get_help("amorphous+atoms"), parent=self)
+
+
+    def get_parameters_from_form(self, form):
+        parameters = {}
+
+        for row in form:
+            if "input" in row and "hidden" in row:
+                temp = (row.split("name=\"")[1]).split("\"")
+                key = temp[0]
+
+                if len(temp) == 2:
+                    value = ((temp[1].split("value=")[1]).split(">")[0]).strip()
+                else:
+                    value = temp[2].strip()
+
+                parameters.update({key : value})
+
+        return parameters
+
+    def get_data_file_from_response(self, response):
+        rows = response.split("\n")
+
+        job_id = None
+        data = None
+
+        for row in rows:
+            if "Job ID" in row:
+                job_id = (row.split("<b>"))[1].split("</b>")[0]
+
+            if not job_id is None:
+                if not job_id+".png" in response:
+                    raise XrayServerException(response)
+
+                if job_id+".dat" in row:
+                    data = HttpManager.send_xray_server_direct_request((row.split("href=\"")[1]).split("\"")[0])
+                    break
+
+        if not data is None:
+            rows = data.split("\n")
+
+            x = []
+            y = []
+
+            for row in rows:
+                values_string = row.strip().split(" ")
+
+                if len(values_string) > 1:
+                    x.append(float(values_string[0].strip()))
+                    y.append(float(values_string[len(values_string)-1].strip()))
+
+            return x, y
+        else:
+            if job_id is None:
+                raise Exception("Job ID not present")
+            else:
+                raise Exception("Empty data file: " + job_id + ".dat")
+
+    def get_plots_from_form(self, application, form):
+        response = HttpManager.send_xray_server_request_GET(application, self.get_parameters_from_form(form))
+
+        return self.get_data_file_from_response(response)
+
+
+    def plot_histo(self, x, y, progressBarValue, tabs_canvas_index, plot_canvas_index, title="", xtitle="", ytitle=""):
+
+        if numpy.sum(y) == 0: raise Exception(title + ": no data to plot (all Y column values==0)")
+
+        if self.plot_canvas[plot_canvas_index] is None:
+            self.plot_canvas[plot_canvas_index] = oasysgui.plotWindow(roi=False, control=False, position=True)
+            self.plot_canvas[plot_canvas_index].setDefaultPlotLines(True)
+            self.plot_canvas[plot_canvas_index].setActiveCurveStyle(color='blue')
+            self.plot_canvas[plot_canvas_index].setYAxisLogarithmic(True)
+
+            self.tabs[tabs_canvas_index].layout().addWidget(self.plot_canvas[plot_canvas_index])
+
+        XRayServerPlot.plot_histo(self.plot_canvas[plot_canvas_index], x, y, title, xtitle, ytitle)
+
+        self.progressBarSet(progressBarValue)
+
+class XrayServerException(Exception):
+
+    response = None
+
+    def __init__(self, response):
+        super().__init__()
+
+        self.response = XrayServerException.clear_response(response)
+
+    @classmethod
+    def clear_response(cls, response):
+        return response.split("<p><b>Download ZIPped results:")[0] + "\n</body></html>"
+
+

oasys2_xrayserver-1.0.0/orangecontrib/xrayserver/widgets/xrayserver/__init__.py

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+"""
+=========
+Associate
+=========
+
+Widgets for association rules.
+
+"""
+
+# Category description for the widget registry
+
+NAME = "X-Ray Server"
+
+DESCRIPTION = "Widgets for X-Ray Server "
+
+BACKGROUND = "#CAB244"
+
+ICON = "icons/xrayserver.png"
+
+PRIORITY = 3001