orGUI 1.0.1__py3-none-any.whl

orgui/app/qutils.py

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+# -*- coding: utf-8 -*-
+# /*##########################################################################
+#
+# Copyright (c) 2020-2024 Timo Fuchs
+#
+# 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.
+#
+# ###########################################################################*/
+__author__ = "Timo Fuchs"
+__copyright__ = "Copyright 2020-2024 Timo Fuchs"
+__license__ = "MIT License"
+__version__ = "1.0.0"
+__maintainer__ = "Timo Fuchs"
+__email__ = "fuchs@physik.uni-kiel.de"
+
+from silx.gui import qt
+
+
+def messagebox_detailed_message(parent, title, text, detailed_text, icon, buttons=qt.QMessageBox.Ok):
+    diag = qt.QMessageBox(icon, title, text, buttons, parent)
+    diag.setDetailedText(detailed_text)
+    return diag.exec()
+
+def critical_detailed_message(parent, title, text, detailed_text, buttons=qt.QMessageBox.Ok):
+    return messagebox_detailed_message(parent, title, text, detailed_text, qt.QMessageBox.Critical, buttons=buttons)
+    
+def warning_detailed_message(parent, title, text, detailed_text, buttons=qt.QMessageBox.Ok):
+    return messagebox_detailed_message(parent, title, text, detailed_text, qt.QMessageBox.Warning, buttons=buttons)
+
+def information_detailed_message(parent, title, text, detailed_text, buttons=qt.QMessageBox.Ok):
+    return messagebox_detailed_message(parent, title, text, detailed_text, qt.QMessageBox.Information, buttons=buttons)
+
+
+
+

orgui/backend/__init__.py

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+# -*- coding: utf-8 -*-
+# /*##########################################################################
+#
+# Copyright (c) 2020-2024 Timo Fuchs
+#
+# 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.
+#
+# ###########################################################################*/
+__author__ = "Timo Fuchs"
+__copyright__ = "Copyright 2020-2024 Timo Fuchs"
+__license__ = "MIT License"
+__version__ = "1.0.0"
+__maintainer__ = "Timo Fuchs"
+__email__ = "fuchs@physik.uni-kiel.de"
+
+__all__ = ['backends', 'scans']

orgui/backend/backends.py

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+# -*- coding: utf-8 -*-
+# /*##########################################################################
+#
+# Copyright (c) 2020-2024 Timo Fuchs
+#
+# 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.
+#
+# ###########################################################################*/
+__author__ = "Timo Fuchs"
+__copyright__ = "Copyright 2020-2024 Timo Fuchs"
+__license__ = "MIT License"
+__version__ = "1.0.0"
+__maintainer__ = "Timo Fuchs"
+__email__ = "fuchs@physik.uni-kiel.de"
+
+import numpy as np
+
+from .scans import Scan
+from datetime import datetime
+import pytz
+
+# --- parse h5node name and return the scan number and name ---
+
+def parseCH5523(obj):
+    ddict = dict() 
+    scanname = obj.local_name
+    scanno = int(scanname.split('_')[-1])
+    ddict['scanno'] = scanno
+    ddict['name'] = obj.local_name.strip('/')
+    return ddict
+
+def parseP212H5(obj):
+    ddict = dict() 
+    scanname = obj.basename
+    scanno, subscanno = scanname.split('.')
+    ddict['scanno'] = int(scanno)
+    ddict['name'] = obj.local_name
+    return ddict
+    
+def parseID31Bliss(obj):
+    ddict = dict() 
+    scanname = obj.local_name
+    scansuffix = scanname.split('_')[-1]
+    scanname_nosuffix = '_'.join(scanname.split('_')[:-1])
+    scanno, subscanno = scansuffix.split('.')
+    ddict['scanno'] = int(scanno)
+    ddict['name'] = obj.local_name
+    return ddict
+    
+# orgui will search for these counters in the Scan object and copy them into the database, if available
+auxillary_counters = ['current', 'potential', 'exposure_time', 'elapsed_time','time', 'srcur', 'mondio', 'epoch']
+    
+# assign the name parser to the beamtime identifiers:
+             
+scannoConverter = {'ch5523': parseCH5523,
+             '20190017': parseP212H5,
+             'ch5700': parseID31Bliss,
+             '20200028': parseP212H5,
+             'ch5918' : parseID31Bliss,
+             'P212_default' : parseP212H5,
+             'id31_default' : parseID31Bliss
+             }
+    
+    
+# --- dates of the beamtimes. Used to identify the beamtimes from the files ---
+
+beamtimes = {'ch5523': (datetime(2018, 9, 22), datetime(2018, 10, 5)),
+             '20190017': (datetime(2019, 12, 8), datetime(2019, 12, 24)),
+             'ch5700': (datetime(2020, 11, 10), datetime(2020, 11, 27)),
+             '20200028': (datetime(2021, 4, 27), datetime(2021, 5, 10)),
+             'ch5918' : (datetime(2021, 7, 18), datetime(2021, 8, 1)),
+             'P212_default' : (datetime(1902, 7, 18), datetime(1903, 8, 1)),
+             'id31_default' : (datetime(2021, 8, 2), datetime(2500, 1, 1)) # all data after 2021/8/2 is automatically detected as ID31 data. You can change this behaviour by changing the beamtime dates. 
+             }
+
+
+
+def localize(dt):
+    if dt.tzinfo is None or dt.tzinfo.utcoffset(dt) is None:
+        grenobletime = pytz.timezone('Europe/Paris')
+        return grenobletime.localize(dt)
+    else:
+        return dt
+             
+def getBeamtimeId(dt):
+    for bt in beamtimes:
+        start, end = beamtimes[bt]
+        if localize(start) <= localize(dt) <= localize(end):
+            return bt
+    else:
+        raise Exception("Didn't find matching beamtime for date %s" % dt.ctime())
+ 
+            
+# add actual backends here, which perform the file reads:
+# They must implement scans.Scan
+
+from .beamline.id31_tools import BlissScan_EBS, Fastscan, BlissScan
+from .beamline.P212_tools import H5Fastsweep
+
+fscans = {'ch5523': BlissScan,
+             '20190017': H5Fastsweep, #probably doesn't work since image names are not saved
+             'ch5700': BlissScan_EBS,
+             '20200028': H5Fastsweep,
+             'ch5918' : BlissScan_EBS,
+             'P212_default' : H5Fastsweep,
+             'id31_default' : BlissScan_EBS
+             }
+
+
+def openScan(btid, ddict):
+    fscancls = fscans[btid]
+    
+    # ideally, now the scan should only be opened with:
+    # fscan = fscancls(ddict['file'], ddict['scanno'])
+    # but this doesn't always work. So handle special cases here
+    
+    if btid == 'ch5523':
+        fscan = fscancls(ddict['file'],ddict['name'])
+        
+        if ddict['name'].startswith('ascan') and 'Pt111_3' in ddict['file']:
+            if fscan.axisname == 'mu':
+                 mu = fscan.mu - 0.055 # misalignment! 
+                 fscan.axis = mu
+                 fscan.mu = mu
+                 print("Correct mu misalignment 0.055 deg,  Pt111_3")
+        
+    elif btid == '20190017' or btid == '20200028' or btid == 'P212_default':
+        fscan = fscancls(ddict['file'],ddict['scanno'])
+    elif btid == 'ch5700' or btid == 'ch5918' or btid == 'id31_default':
+        if 'node' in ddict:
+            fscan = fscancls(ddict['node'],ddict['scanno'], loadimg=False)
+        else:
+            fscan = fscancls(ddict['file'],ddict['scanno'], loadimg=False)
+    else:
+        try:
+            fscan = fscancls(ddict['file'], ddict['scanno'])
+        except Exception:
+            raise ValueError("Did not find matching scan in backends for beamtime id %s" % btid)
+    return fscan 
+
+

orgui/backend/beamline/ID31DiffractLinTilt.py

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+# -*- coding: utf-8 -*-
+
+"""ID31 beamline code.
+
+Used for this software with permission from Jakub Drnec
+
+"""
+
+import numpy as np
+
+class ID31DiffractLinTilt(object):
+    """
+    ID31DiffractLinTilt: transforms linear motors into tilt motor (angular)
+
+    Some angular motors are mechanically moved through linear translations.
+    
+    muoffset has to be set for each experiment since it is dependent on
+    the diffractometer alignment!
+    
+    Adapted version from the ID31 beamline code.
+    """
+    def __init__(self, *args, **kwargs):
+        self.config = {}
+        self.config['a'] = 938
+        self.config['b'] = 400
+        self.config['muoffset'] = -0.06442416994811659
+
+    @property
+    def a(self):
+        return self.config.get("a", float)
+
+    @property
+    def b(self):
+        return self.config.get("b", float)
+        
+    @property
+    def muoffset(self):
+        return self.config.get("muoffset", float)
+
+    def c(self, a=None, b=None):
+        a = self.a if a is None else a
+        b = self.b if b is None else b
+        return np.sqrt(np.square(a) + np.square(b))
+
+    def d(self, a=None, b=None):
+        a = self.a if a is None else a
+        b = self.b if b is None else b
+        return np.arctan(b / a)
+
+    def calc_from_real(self, positions_dict):
+        a, b = self.a, self.b
+        c, d = self.c(a, b), self.d(a, b)
+        a2, c2 = np.square(a), np.square(c)
+        linear = positions_dict["linear"]
+        bc2 = np.square(b + linear)
+        tilt = np.arccos((a2 + c2 - bc2) / (2 * a * c)) - d
+        return dict(tilt=np.rad2deg(tilt))
+
+    def calc_to_real(self, positions_dict):
+        a, b = self.a, self.b
+        c, d = self.c(a, b), self.d(a, b)
+        a2, c2 = np.square(a), np.square(c)
+        tilt = np.deg2rad(positions_dict["tilt"])
+        bc = np.sqrt(a2 + c2 - 2 * a * c * np.cos(tilt + d))
+        linear = bc - b
+        return dict(linear=linear)
+        
+    def linai_to_mu(self,linai):
+        positions = {'linear' : linai}
+        tilt = self.calc_from_real(positions)
+        return tilt["tilt"] - self.muoffset
+        
+    def mu_to_linai(self,mu):
+        ai = mu + self.muoffset #np.linspace(-1.0,1,11) + muoffset
+        tilts = {'tilt' : ai}
+        pos = self.calc_to_real(tilts)
+        return pos['linear']