uedgetools 1.3.2__tar.gz → 1.3.3__tar.gz

{uedgetools-1.3.2/src/uedgetools.egg-info → uedgetools-1.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: uedgetools
-Version: 1.3.2
+Version: 1.3.3
 Summary: A utility tool for the UEDGE multi-fluid plasma-edge code
 Author-email: Andreas Holm <holm10@llnl.gov>
 License:                   GNU LESSER GENERAL PUBLIC LICENSE
@@ -524,9 +524,10 @@ Requires-Dist: h5py
 Requires-Dist: pyaml
 Requires-Dist: Forthon
 Requires-Dist: matplotlib
+Requires-Dist: shapely
 Requires-Dist: h5pickle
 Requires-Dist: PyQt5
-Requires-Dist: bayesian-optimization
+Requires-Dist: bayesian-optimization>=3
 Provides-Extra: parallel
 Requires-Dist: inspect; extra == "parallel"
 Requires-Dist: uuid; extra == "parallel"

{uedgetools-1.3.2 → uedgetools-1.3.3}/pyproject.toml

@@ -25,9 +25,10 @@ dependencies = [
     "pyaml",
     "Forthon",
     "matplotlib",
+    "shapely",
     "h5pickle",
     "PyQt5",
-    "bayesian-optimization",
+    "bayesian-optimization >= 3",
 ]
 
 [project.optional-dependencies]

{uedgetools-1.3.2 → uedgetools-1.3.3/src/uedgetools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: uedgetools
-Version: 1.3.2
+Version: 1.3.3
 Summary: A utility tool for the UEDGE multi-fluid plasma-edge code
 Author-email: Andreas Holm <holm10@llnl.gov>
 License:                   GNU LESSER GENERAL PUBLIC LICENSE
@@ -524,9 +524,10 @@ Requires-Dist: h5py
 Requires-Dist: pyaml
 Requires-Dist: Forthon
 Requires-Dist: matplotlib
+Requires-Dist: shapely
 Requires-Dist: h5pickle
 Requires-Dist: PyQt5
-Requires-Dist: bayesian-optimization
+Requires-Dist: bayesian-optimization>=3
 Provides-Extra: parallel
 Requires-Dist: inspect; extra == "parallel"
 Requires-Dist: uuid; extra == "parallel"

{uedgetools-1.3.2 → uedgetools-1.3.3}/src/uedgetools.egg-info/requires.txt

@@ -4,9 +4,10 @@ h5py
 pyaml
 Forthon
 matplotlib
+shapely
 h5pickle
 PyQt5
-bayesian-optimization
+bayesian-optimization>=3
 
 [parallel]
 inspect

{uedgetools-1.3.2 → uedgetools-1.3.3}/src/uetools/UeCase/Input.py

@@ -60,11 +60,9 @@ class Input:
 
         def recursive_readhdf5(ret, setup, group=[], root=None):
             if len(group) > 0:
-                lastgroup=group[0]
+                lastgroup = group[0]
                 # Conditional to avoid unnecessary nesting
-                if ((len(group) > 1) and \
-                    (group[-1] == group[-2]) \
-                ):
+                if (len(group) > 1) and (group[-1] == group[-2]):
                     group.pop(-1)
                 else:
                     for subgroup in group:
@@ -256,7 +254,9 @@ class Input:
                         try:
                             self.setue(group[-1], dictobj)
                         except KeyError as e:
-                            print(f"WARNING Could not set '{group[-1]}' to '{dictobj}'. Reason: {e}")
+                            print(
+                                f"WARNING Could not set '{group[-1]}' to '{dictobj}'. Reason: {e}"
+                            )
 
                 else:  # Set calls to restore diffusivities
                     if (group[-1] == "savefile") and (
@@ -264,28 +264,32 @@ class Input:
                     ):
                         pass
                     elif group[-1] in ["casename", "commands", "chgstate_format"]:
-                        if group[-1]=="casename":
+                        if group[-1] == "casename":
                             self.casename_set = True
                         self.info[group[-1]] = dictobj
                     elif group[-1] in [
-                            "userdifffname", 
-                            "radialdifffname",
-                            "diff_file",
-                            "savefile",
+                        "userdifffname",
+                        "radialdifffname",
+                        "diff_file",
+                        "savefile",
                     ]:
                         if isinstance(dictobj, (bytes, bytearray)):
                             dictobj = dictobj.decode("UTF-8")
-                        if dictobj is not False:
-                            self.info[group[-1]] = "/".join(
-                                [self.info["location"], dictobj]
-                        )
-                    elif group[-1] in self.variables["omit"]:# ["lynix", "lyphix", "lytex", "lytix"]:
+                        if dictobj != False:
+                            self.info[group[-1]] = os.path.join(
+                                self.info["location"], dictobj
+                            )
+                    elif (
+                        group[-1] in self.variables["omit"]
+                    ):  # ["lynix", "lyphix", "lytex", "lytix"]:
                         pass
                     else:
                         if isinstance(dictobj, (bytes, bytearray)):
                             dictobj = dictobj.decode("UTF-8")
                         try:
-                            self.info[group[-1]] = os.path.join(self.info["location"], dictobj)
+                            self.info[group[-1]] = os.path.join(
+                                self.info["location"], dictobj
+                            )
                         except TypeError:
                             # dictobj may be e.g. bool that can't be joined with path
                             self.info[group[-1]] = self.info["location"]
@@ -347,19 +351,22 @@ class Input:
             if isinstance(self.info["savefile"], bytes):
                 self.info["savefile"] = self.info["savefile"].decode("UTF-8")
             if self.info["restored_from_hdf5"] is True:
-
                 prfile = setupfile
-                if len(prfile.split('/'))>3:
-                    prfile = ".../{}".format('/'.join(prfile.split('/')[-3:]))
+                if len(prfile.split("/")) > 3:
+                    prfile = ".../{}".format("/".join(prfile.split("/")[-3:]))
                 print("=================================================")
                 print("Restoring case from HDF5 file:")
                 print("  Rate dirs read from .uedgerc")
                 print("  Grid read from {}".format(prfile))
-                self.info["diffusivity_file"] = os.path.join(self.info["location"], setupfile)
+                self.info["diffusivity_file"] = os.path.join(
+                    self.info["location"], setupfile
+                )
 
             # Override with diff_file maually defined diff_file upon
             if diff_file is not None:
-                self.info["diffusivity_file"] = os.path.join(self.info["location"], diff_file)
+                self.info["diffusivity_file"] = os.path.join(
+                    self.info["location"], diff_file
+                )
             # Otherwise, try setting accoridng to input
             else:
                 # diff_file takes precedence
@@ -371,15 +378,13 @@ class Input:
                         if (self.info["radialdifffname"] is not None) and (
                             self.info["radialdifffname"] is not False
                         ):
-                            self.info["diffusivity_file"] = \
-                                    self.info['radialdifffname']
+                            self.info["diffusivity_file"] = self.info["radialdifffname"]
                         del self.info["radialdifffname"]
                     if "userdifffname" in self.info:
                         if (self.info["userdifffname"] is not None) and (
                             self.info["userdifffname"] is not False
                         ):
-                            self.info["diffusivity_file"] = \
-                                    self.info["userdifffname"]
+                            self.info["diffusivity_file"] = self.info["userdifffname"]
                         del self.info["userdifffname"]
             if (self.info["diffusivity_file"] is None) and (
                 self.getue("isbohmcalc") in [0, 2]
@@ -387,8 +392,8 @@ class Input:
                 self.info["diffusivity_file"] = self.info["savefile"]
 
                 prfile = self.info["diffusivity_file"]
-                if len(prfile.split('/'))>3:
-                    prfile = ".../{}".format('/'.join(prfile.split('/')[-3:]))
+                if len(prfile.split("/")) > 3:
+                    prfile = ".../{}".format("/".join(prfile.split("/")[-3:]))
                 print(
                     "No diffusivity-file supplied: reading from "
                     + 'save-file "{}"'.format(prfile)
@@ -396,8 +401,8 @@ class Input:
             # Set diffusivities based on file if model requires profiles
             if self.getue("isbohmcalc") == 0:
                 prfile = self.info["diffusivity_file"]
-                if len(prfile.split('/'))>3:
-                    prfile = ".../{}".format('/'.join(prfile.split('/')[-3:]))
+                if len(prfile.split("/")) > 3:
+                    prfile = ".../{}".format("/".join(prfile.split("/")[-3:]))
                 print(
                     "  User-specified diffusivities read from HDF5 "
                     + 'file "{}"'.format(prfile)
@@ -433,7 +438,7 @@ class Input:
         if restoresave is True:
             if (self.info["savefile"] is None) and (self.get("restart") == 1):
                 if self.info["casename"] is not None:
-                    for suffix in ["h5","hdf5"]:
+                    for suffix in ["h5", "hdf5"]:
                         savefile = ".".join([self.info["casename"], suffix])
                         if exists(savefile):
                             self.info["savefile"] = savefile
@@ -442,8 +447,9 @@ class Input:
             if exists(self.info["savefile"]):
                 self.savefuncs.load_state(self.info["savefile"], **kwargs)
             else:
-                raise ValueError("Could not open save-file '{}'".format(\
-                    self.info["savefile"]))
+                raise ValueError(
+                    "Could not open save-file '{}'".format(self.info["savefile"])
+                )
         if uedge_is_installed and not self.info["inplace"]:
             self.tracker.get_uevars()
         # NOTE: Get the hashes before running any commands. This way,

{uedgetools-1.3.2 → uedgetools-1.3.3}/src/uetools/UeDashboard/Dashboard.py

@@ -500,6 +500,7 @@ class CaseDashboard(QWidget):
         ==========================="""
     def _createVarButtons(self):
         from numpy import sum, ndarray
+        self.buttonsetup = True
         self.buttons = {
             'layout': QGridLayout(),
             'title': QLabel(self.title("Plots")),
@@ -537,8 +538,8 @@ class CaseDashboard(QWidget):
             cols[int(i/maxbuttons)].addWidget(
                 self.buttons['items'][key], 
             )
-            # TODO: Implement smarter check to deactivat buttons
-            buttonvar = self.get(key)
+            test = True
+            buttonvar = self.__getattribute__(f'plot_{key}')()
             if buttonvar is not None:
                 vis = True
                 if len(buttonvar.shape) == 3:
@@ -548,11 +549,12 @@ class CaseDashboard(QWidget):
                     if varsum == 0:
                         self.buttons['items'][key].setEnabled(False)
                 else:
-                    if sum(self.get(key)) == 0:
+                    if sum(buttonvar) == 0:
                         self.buttons['items'][key].setEnabled(False)
                 i += 1
         self.checkedButton = self.buttongroup.button(0)
         self.checkedButton.setChecked(True)
+        test = False
 
         # Add drop-down
         self.buttons['items']['dropdown'] = QComboBox()
@@ -592,6 +594,7 @@ class CaseDashboard(QWidget):
         for i in range(len(cols)):
             self.buttons['layout'].addLayout(cols[i], 1, i, 1, 1)
         self.buttons['layout'].addLayout(custom, 2,0,1,len(cols))
+        self.buttonsetup = False
 
 
 
@@ -1010,114 +1013,162 @@ class CaseDashboard(QWidget):
         self.enable_ionradio(False)
         self.uncheck_buttons()
 
-    def plot_te(self):
+    def plot_te(self):  
+        var = self.get('te')/1.602e-19
+        if self.buttonsetup:
+            return var
         self.plot_driver(
-            self.get('te')/1.602e-19,
+            var,
             'Electron temperature [eV]',
         )
         self.lastfunc = self.plot_te
 
     def plot_ti(self):
+        var = self.get('ti')/1.602e-19
+        if self.buttonsetup:
+            return var
         self.plot_driver(
-            self.get('ti')/1.602e-19,
+            var,
             'Ion temperature [eV]',
         )
         self.lastfunc = self.plot_ti
 
     def plot_tg(self):
+        var = self.get('tg')/1.602e-19
+        if self.buttonsetup:
+            return var
         self.plot_driver(
-            self.get('tg')/1.602e-19,
+            var,
             'Gas temperature [eV]',
             'gas'
         )
         self.lastfunc = self.plot_tg
 
     def plot_ne(self):
+        var = self.get('ne')
+        if self.buttonsetup:
+            return var
         self.plot_driver(
-            self.get('ne'),
+            var,
             r'Electron density [m$\mathrm{{}^{-3}}$]',
         )
         self.lastfunc = self.plot_ne
 
     def plot_ni(self):
+        var = self.get('ni')
+        if self.buttonsetup:
+            return var
         self.plot_driver(
-            self.get('ni'),
+            var,
             r'Ion density [m$\mathrm{{}^{-3}}$]',
             'ion'
         )
         self.lastfunc = self.plot_ni
 
     def plot_ng(self):
+        var = self.get('ng')
+        if self.buttonsetup:
+            return var
         self.plot_driver(
-            self.get('ng'),
+            var,
             r'Gas density [m$\mathrm{{}^{-3}}$]',
             'gas'
         )
         self.lastfunc = self.plot_ng
 
     def plot_phi(self):
+        var = self.get('phi')
+        if self.buttonsetup:
+            return var
         self.plot_driver(
-            self.get('phi'),
+            var,
             'Electrical potential [V]',
         )
         self.lastfunc = self.plot_phi
 
     def plot_prad(self):
+        if self.get('prad').shape == self.get('pradhyd').shape:
+            var = self.get('prad')+self.get('pradhyd')
+        else:
+            var = self.get('pradhyd')
+        if self.buttonsetup:
+            return var
         self.plot_driver(
-            self.get('prad')+self.get('pradhyd'),
+            var,
             r'Total radiated power [W/m$\mathrm{{}^{-3}}$]',
         )
         self.lastfunc = self.plot_prad
 
     def plot_pradhyd(self):
+        var = self.get('pradhyd')
+        if self.buttonsetup:
+            return var
         self.plot_driver(
-            self.get('pradhyd'),
+            var,
             r'Hydrogenic radiated power [W/m$\mathrm{{}^{-3}}$]',
         )
         self.lastfunc = self.plot_pradhyd
 
     def plot_pradimp(self):
+        var = self.get('prad')
+        if self.buttonsetup:
+            return var
         self.plot_driver(
-            self.get('prad'),
+            var,
             r'Impurity radiated power [W/m$\mathrm{{}^{-3}}$]',
         )
         self.lastfunc = self.plot_pradimp
 
     def plot_psorc(self):
+        var = self.get('psorc')
+        if self.buttonsetup:
+            return var
         self.plot_driver(
-            self.get('psorc'),
+            var,
             'Ion ionization source [parts/s]',
             'ion'
         )
         self.lastfunc = self.plot_psorc
 
     def plot_psorgc(self):
+        var = self.get('psorgc')
+        if self.buttonsetup:
+            return var
         self.plot_driver(
-            self.get('psorgc'),
+            var,
             'Gas ionization sink [parts/s]',
             'gas'
         )
         self.lastfunc = self.plot_psorgc
 
     def plot_psorxrc(self):
+        var = self.get('psorxrc')
+        if self.buttonsetup:
+            return var
         self.plot_driver(
-            self.get('psorxrc'),
+            var,
             'Ion recombination + CX sink [parts/s]',
             'ion'
         )
         self.lastfunc = self.plot_psorxrc
 
     def plot_psorrgc(self):
+        var = self.get('psorrgc')
+        if self.buttonsetup:
+            return var
         self.plot_driver(
-            self.get('psorrgc'),
+            var,
             'Gas recombination source [parts/s]',
             'gas'
         )
         self.lastfunc = self.plot_psorrgc
 
     def plot_psorcxg(self):
+        var = self.get('psorcxg')
+        if self.buttonsetup:
+            return var
         self.plot_driver(
-            self.get('psorcxg'),
+            var,
             'Gas CX source [parts/s]',
             'gas'
         )
@@ -1656,10 +1707,11 @@ class MainMenu(QMainWindow):
     def openHDF5(self):#, caseobj=None):
         from uetools import Case
         # Logic for opening an existing file goes here...
-        if 1==0:
+        if 1==1:
             file = QFileDialog.getOpenFileName(self, 'Open UETOOLS save', 
-            self.lastpath, "All files (*.*)")[0]
-            self.lastpath = "/".join(file.split("/")[:-1])
+            self.lastpath, "All files (*.*)",  options=QFileDialog.DontUseNativeDialog)[0]
+            self.lastpath = "/".join(file.split("/")[:-1],
+            )
         else:
             file = "/Users/holm10/Documents/fusion/uedge/src/"+\
                     "UETOOLS/dashboard_test/testcase_hires/nc20.hdf5"
@@ -1691,7 +1743,9 @@ class MainMenu(QMainWindow):
             )
             print("USING TEST DATABASE")
         else:
-            path = str(QFileDialog.getExistingDirectory(self, "Select Directory"))
+            path = str(QFileDialog.getExistingDirectory(self, "Select Directory",
+                 options=QFileDialog.DontUseNativeDialog
+            ))
             if len(path) == 0:
                 return
             name = path.split('/')[-1]
@@ -1856,7 +1910,7 @@ if __name__ == "__main__":
     matplotlib.use('Qt5Agg')
     app = QApplication(sys.argv)
     win = MainMenu()
-    win.openHDF5()
+#    win.openHDF5()
     win.show()
     sys.exit(app.exec_())
 #else:

{uedgetools-1.3.2 → uedgetools-1.3.3}/src/uetools/UeDiagnostics/Diagnostics.py

@@ -760,6 +760,13 @@ class Spectrometer:
             # Associate list to dict key
             self.emission[l] = emission_chord
 
+    def chord_integral_field(self, field):
+        integrals = []
+        for chord in self.chords:
+            integrals.append(chord.integrate_field(field))
+        return integrals
+        
+
     def plot_chord_integral(
         self, field, ax=None, linestyle="-", marker="o", color="k", x=None
     ):
@@ -798,10 +805,8 @@ class Spectrometer:
         if x is None:
             x = range(1, len(self.chords) + 1)
         # TODO: Figure out what to use as X-axis
-        integrals = []
-        for chord in self.chords:
-            integrals.append(chord.integrate_field(field))
 
+        integrals = self.chord_integral_field(field)
         ax.plot(x, integrals, linestyle=linestyle, marker=marker, color=color)
 
         return ax.get_figure()
@@ -1209,7 +1214,12 @@ class Grid:
         self.area = coverage_union_all(geometries)
         # Create and store Polygon for core
         corepts = []
-        for nxpt in range(case.get("nxpt")):
+        nnxpt = case.get('nxpt', verbose=False)
+        if nnxpt is None:
+            nnxpt = 1
+            if case.plot.dnull:
+                nnxpt = 2
+        for nxpt in range(nnxpt):
             for ix in range(case.get("ixpt1")[nxpt] + 1, case.get("ixpt2")[nxpt] + 1):
                 corepts.append(
                     [

{uedgetools-1.3.2 → uedgetools-1.3.3}/src/uetools/UePlot/CasePlot.py

@@ -603,19 +603,21 @@ class Caseplot(Plot):
             ax.plot((ixpt1[ixpt]+0.5,ixpt1[ixpt]+0.5), (-0.5,iysptrx1[ixpt]+.5), 'k-', linewidth=1.5)
             ax.plot((ixpt2[ixpt]+0.5,ixpt2[ixpt]+0.5), (-0.5,iysptrx2[ixpt]+.5), 'k-', linewidth=1.5)
 
+        for xpatch in self.get('rangechunk'):
+            ax.add_patch(Polygon( [(xpatch[0]-.5,xpatch[2]-.5),(xpatch[0]-.5,xpatch[3]+.5),(xpatch[1]+.5, xpatch[3]+.5),(xpatch[1]+.5, xpatch[2]-0.5)],
+                 closed=True, edgecolor='k', alpha=0.3, linestyle='--', linewidth=2, color=next(colors)))
+
         for ixpt in range(nxpt):
             for icut in range(self.get('Nxptchunks')[ixpt]):
                 for ii in range(2):
                     xpatch = rangexptchunk[ixpt, ii, icut]
                     ax.add_patch(Polygon( [(xpatch[0]-.5,xpatch[2]-.5),(xpatch[0]-.5,xpatch[3]+.5),(xpatch[1]+.5, xpatch[3]+.5),(xpatch[1]+.5, xpatch[2]-0.5)],
-                    closed=True, edgecolor='k', facecolor='red'))
+                    closed=True, edgecolor='k', facecolor='red', linestyle='-', linewidth=1))
 
-        for xpatch in self.get('rangechunk'):
-            ax.add_patch(Polygon( [(xpatch[0]-.5,xpatch[2]-.5),(xpatch[0]-.5,xpatch[3]+.5),(xpatch[1]+.5, xpatch[3]+.5),(xpatch[1]+.5, xpatch[2]-0.5)],
-                 closed=True, edgecolor='k', alpha=0.3, linestyle='--', linewidth=2, color=next(colors)))
 
 
         f.show()
+        return f
 
 
     def variablemesh(self, z=None, **kwargs):

{uedgetools-1.3.2 → uedgetools-1.3.3}/src/uetools/UeUtils/AboutSetup.py

@@ -111,7 +111,7 @@ class AboutSetup:
         ionarray = []
         for i in range(nisp):
             charge = "{}".format(
-                ("+" + str(int(zi[i]))) * (zi[i] > 0) + "0" * (zi[i] == 0)
+                ("+" + str(int(zi[i]))) * bool(zi[i] > 0) + "0" * bool(zi[i] == 0)
             )
             sign = "".join(
                 (x for x in elements[znuclin[i]][minu[i]] if not x.isdigit())

uedgetools-1.3.3/src/uetools/VERSION

@@ -0,0 +1 @@
+1.3.3

uedgetools-1.3.2/src/uetools/VERSION

@@ -1 +0,0 @@
-1.3.2