orGUI 1.0.1__py3-none-any.whl

orgui/backend/scans.py

@@ -0,0 +1,95 @@
+# -*- 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
+
+
+class Scan():
+
+    def __init__(self,hdffilepath_orNode=None, scanno=None):
+        self.axisname = None # either "th" or "mu"
+        self.axis = None # value of either "th" or "mu"
+        self.th = 0. # or self.mu, depending on scanaxis
+        self.omega = 0. # = -1*th
+        self.title = "generic_scan"
+        # for mu-scan you must provide a value for omega/theta 
+
+    def __len__(self):
+        raise NotImplementedError()
+
+    def get_raw_img(self, i):
+        raise NotImplementedError()
+        
+
+
+class h5_Image:
+    
+    def __init__(self, data):
+        
+        self.img = data 
+        self.motors = dict()
+        self.counters = dict()
+
+
+class SimulationScan(Scan):
+
+    def __init__(self, detshape, axismin, axismax, points, axis='th', fixed=0.):
+        
+        self.shape = detshape
+        self.axisname = axis
+        self.axis = np.linspace(axismin,axismax,points)
+        if axis == 'th':
+            self.th = self.axis
+            self.omega = -1*self.th
+            self.mu = fixed
+        elif axis == 'mu':
+            self.mu = self.axis
+            self.th = fixed
+            self.omega = -1*self.th
+        else:
+            raise ValueError("%s is not an implemented scan axis." % axis)
+        self.nopoints = points
+        
+        self.images = np.zeros((points,*detshape))
+        self.title = "sim ascan %s %s %s %s" % (self.axisname,axismin,axismax,points)
+        
+    def __len__(self):
+        return self.nopoints
+        
+    def get_raw_img(self, i):
+        return h5_Image(self.images[i])
+        
+    def set_raw_img(self, i, data): #for intensity simulation in the future.
+        self.images[i] = data
+        
+        
+

orgui/backend/udefaults.py

@@ -0,0 +1,163 @@
+# -*- 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 ..datautils.xrayutils import HKLVlieg
+from ..datautils import util
+
+def defaultU_GID(ubCalculator):
+    """Sets a default U matrix for Grazing incidence surface diffraction geometry.
+    
+    Geometry:
+    L along z axis in alpha frame
+    K along x axis in alpha frame
+    for chi = 0°, phi = 0°, omega = 0° (omega = -theta)
+    
+    Aligns crystal L axis along omega rotation axis. 
+    Alpha tilts this rotation axis. Typically alpha is equal to the angle of incidence.
+
+    """
+    # Compute the two reflections' reciprical vectors in the
+    # cartesian crystal frame (hc = B @ hkl)
+    h1c = ubCalculator.lattice.reciprocalVectorCart([0.,0.,1.]).flatten() # for hkl = (0, 0, 1)
+    h2c = ubCalculator.lattice.reciprocalVectorCart([0.,1.,0.]).flatten() # for hkl = (0, 1, 0)
+    
+    # Calculate the sample rotation matrices
+    
+    chi1 = np.deg2rad(0.)
+    phi1 = np.deg2rad(0.)
+    omega1 = np.deg2rad(0.)
+    
+    chi2 = np.deg2rad(0.)
+    phi2 = np.deg2rad(0.)
+    omega2 = np.deg2rad(0.)
+    
+    # [ALPHA, DELTA, GAMMA, OMEGA, CHI, PHI]
+    pos1 = np.array([None, None, None, omega1, chi1, phi1])
+    pos2 = np.array([None, None, None, omega2, chi2, phi2])
+    
+    _,_,_, OM1, CHI1, PHI1 = HKLVlieg.createVliegMatrices(pos1) # rotation matrices
+    _,_,_, OM2, CHI2, PHI2 = HKLVlieg.createVliegMatrices(pos2) # rotation matrices
+    
+    # define reference directions in alpha frame
+    
+    Qalp1 = np.array([0.,0.,1.]) * np.linalg.norm(h1c) # reference 1:  z direction
+    Qalp2 = np.array([1.,0.,0.]) * np.linalg.norm(h2c) # reference 2:  x direction
+    
+    # Transform Qalp in Qphi
+    # hint: matrix inverse of rotation matrices is the transpose (T)
+    Qphi1 = PHI1.T @ CHI1.T @ OM1.T @ Qalp1
+    Qphi2 = PHI2.T @ CHI2.T @ OM2.T @ Qalp2
+    
+    # 1: primary vector, 2: secondary vector
+    
+    U, stats = HKLVlieg.UBCalculator.calc_U_from_vectors(Qphi1, Qphi2, h1c, h2c)
+    
+    ubCalculator.setU(U)
+    
+    return ubCalculator
+
+def defaultU_TSD(ubCalculator):
+    """Sets a default U matrix for Transmission Surface Diffraction geometry.
+    
+    Geometry:
+    L along y axis in laboratory frame (along beam direction) at omega = 0°
+    K along z axis in laboratory frame
+    for chi = 90°
+    phi = 0°
+    alpha = 0°
+    
+    In TSD mode, the crystal L axis points towards the beam direction at one 
+    specific omega value as described here:
+    
+    Transmission Surface Diffraction for Operando Studies of Heterogeneous Interfaces
+    Finn Reikowski, Tim Wiegmann, Jochim Stettner, Jakub Drnec, Veijo Honkimäki, Fouad Maroun, Philippe Allongue, and Olaf M. Magnussen
+    The Journal of Physical Chemistry Letters 2017 8 (5), 1067-1071
+    DOI: 10.1021/acs.jpclett.7b00332
+
+    """
+    # Compute the two reflections' reciprical vectors in the
+    # cartesian crystal frame (hc = B @ hkl)
+    h1c = ubCalculator.lattice.reciprocalVectorCart([0.,0.,1.]).flatten() # for hkl = (0, 0, 1)
+    h2c = ubCalculator.lattice.reciprocalVectorCart([0.,1.,0.]).flatten() # for hkl = (0, 1, 0)
+    
+    # Calculate the sample rotation matrices
+    
+    chi1 = np.deg2rad(90.)
+    phi1 = np.deg2rad(0.)
+    omega1 = np.deg2rad(0.)
+    alpha1 = np.deg2rad(0.)
+    
+    chi2 = np.deg2rad(90.)
+    phi2 = np.deg2rad(0.)
+    omega2 = np.deg2rad(0.)
+    alpha2 = np.deg2rad(0.)
+    
+    # [ALPHA, DELTA, GAMMA, OMEGA, CHI, PHI]
+    pos1 = np.array([alpha1, None, None, omega1, chi1, phi1])
+    pos2 = np.array([alpha2, None, None, omega2, chi2, phi2])
+    
+    A1,_,_, OM1, CHI1, PHI1 = HKLVlieg.createVliegMatrices(pos1) # rotation matrices
+    A2,_,_, OM2, CHI2, PHI2 = HKLVlieg.createVliegMatrices(pos2) # rotation matrices
+    
+    # define reference directions in laboratory frame
+    
+    Qlab1 = np.array([0.,1.,0.]) * np.linalg.norm(h1c) # reference 1:  y direction
+    Qlab2 = np.array([0.,0.,1.]) * np.linalg.norm(h2c) # reference 2:  z direction
+    
+    # Transform Qlab in Qphi
+    # hint: matrix inverse of rotation matrices is the transpose (T)
+    Qphi1 = PHI1.T @ CHI1.T @ OM1.T @ A1.T @ Qlab1
+    Qphi2 = PHI2.T @ CHI2.T @ OM2.T @ A2.T @ Qlab2
+    
+    # 1: primary vector, 2: secondary vector
+    
+    U, stats = HKLVlieg.UBCalculator.calc_U_from_vectors(Qphi1, Qphi2, h1c, h2c)
+    
+    ubCalculator.setU(U)
+    
+    return ubCalculator
+    
+def manualU(ubCalculator):
+    U = np.array([[1., 0., 0.],
+                  [0., 1., 0.],
+                  [0., 0., 1.]])
+    # could also do something like 
+    # U = util.z_rotation(np.deg2rad(45.))
+    ubCalculator.setU(U)
+    return ubCalculator
+
+
+u_defaults = {
+    'Grazing incidence' : defaultU_GID,
+    'Transmission' : defaultU_TSD,
+    'manual U' : manualU
+}

orgui/backend/universalScanLoader.py

@@ -0,0 +1,105 @@
+# -*- coding: utf-8 -*-
+# /*##########################################################################
+#
+# Copyright (c) 2024 Finn Schroeter
+#
+# 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__ = "Finn Schroeter"
+__credits__ = ['Finn Schroeter']
+__copyright__ = "Copyright 2024 Finn Schroeter"
+__license__ = "MIT License"
+__version__ = "1.0.0"
+
+import re
+import os
+import fabio
+import numpy as np
+
+from .scans import h5_Image
+
+class ImportImagesScan():
+
+    def __init__(self, imgpath):
+        self.filename = imgpath
+
+        self.inpath = self.find_files()
+
+        img_data = fabio.open(self.inpath[0] + self.inpath[1][0])
+        self.shape = (img_data.data.shape[0], img_data.data.shape[1])
+
+        self.FramesPerFile = img_data.nframes
+        if self.FramesPerFile > 1:
+            last_file = fabio.open(self.inpath[0] + self.inpath[1][-1])
+            self.FramesLastFile = last_file.nframes
+        else:
+            self.FramesLastFile = self.FramesPerFile
+
+        self.images = np.zeros((1,*self.shape))
+
+        self.axisname = ''
+        self.axis = [0]
+        self.th = 0
+        self.omega = 0
+        self.mu = 0
+
+        self.title = "manually loaded scan" 
+
+        self.nopoints = (len(self.inpath[1])-1)*self.FramesPerFile + self.FramesLastFile
+
+
+    def find_files(self):
+        re_str = re.compile(r'_\d+' + os.path.splitext(self.filename)[1]) #define search string. It matches a file source with syntax name_0000i.extension -> may need to be adapted 
+        selected_directory = os.path.dirname(os.path.abspath(self.filename))
+        filenames = ''.join(os.listdir(selected_directory))
+
+        found_scanfiles = re_str.findall(filenames) #list of found filenames (suffix only)
+        suffix = re_str.findall(self.filename)[0]
+        imagePrefix = self.filename.removesuffix(suffix)
+
+        #found_scannrs = [e[1:-4] for e in found_scanfiles] #only the scan numbers, eg. 00015
+
+        return [imagePrefix,found_scanfiles]
+
+    def set_axis(self,axismin,axismax,axis,fixedAxisValue):
+        self.axis = np.linspace(axismin,axismax,self.nopoints)
+        self.axisname = axis
+        if axis == 'th':
+            self.th = self.axis
+            self.omega = -1*self.th
+            self.mu = fixedAxisValue
+
+        
+    def __len__(self):
+        return self.nopoints
+        
+    def get_raw_img(self, i):
+        if self.FramesPerFile > 1:
+            index = i // self.FramesPerFile
+            frame = i % self.FramesPerFile
+            img_data = fabio.open(self.inpath[0] + self.inpath[1][index]).get_frame(frame)
+        else:
+            img_data = fabio.open(self.inpath[0] + self.inpath[1][i])
+
+        return h5_Image(img_data.data)
+        
+    def set_raw_img(self, i, data): #for intensity simulation in the future.
+        self.images[i] = data
+        

orgui/datautils/__init__.py

@@ -0,0 +1,32 @@
+# -*- 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__ = ['util']