pypsbuilder 2.3.6__tar.gz → 2.4.0__tar.gz

{pypsbuilder-2.3.6 → pypsbuilder-2.4.0}/CHANGELOG.md

@@ -1,6 +1,12 @@
 # Changelog
 All notable pypsbuilder changes.
 
+## [2.4.0] - 2023-12-21
+### Fixed
+ - important collect_grid_data bug causing isopleths twisting fixed. 
+ - collect_ptpath missing field check added
+ - remove_grid_data method added
+ - isopleths bivariate spline method added
 ## [2.3.6] - 2023-12-13
 ### Added
  - search_composition method added to PTPS to find best estimate for isopleths intersection

{pypsbuilder-2.3.6 → pypsbuilder-2.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pypsbuilder
-Version: 2.3.6
+Version: 2.4.0
 Summary: THERMOCALC front-end for constructing and analyzing PT pseudosections
 Home-page: https://github.com/ondrolexa/pypsbuilder
 Author: Ondrej Lexa
@@ -88,6 +88,12 @@ pypsbuilder is free software: you can redistribute it and/or modify it under the
 # Changelog
 All notable pypsbuilder changes.
 
+## [2.4.0] - 2023-12-21
+### Fixed
+ - important collect_grid_data bug causing isopleths twisting fixed. 
+ - collect_ptpath missing field check added
+ - remove_grid_data method added
+ - isopleths bivariate spline method added
 ## [2.3.6] - 2023-12-13
 ### Added
  - search_composition method added to PTPS to find best estimate for isopleths intersection

{pypsbuilder-2.3.6 → pypsbuilder-2.4.0}/docs/conf.py

@@ -20,9 +20,9 @@
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath('.'))
-sys.path.insert(0, os.path.abspath('..'))
-sys.path.insert(0, os.path.abspath('../'))
+sys.path.insert(0, os.path.abspath("."))
+sys.path.insert(0, os.path.abspath(".."))
+sys.path.insert(0, os.path.abspath("../"))
 
 
 # -- General configuration ------------------------------------------------
@@ -35,42 +35,49 @@ sys.path.insert(0, os.path.abspath('../'))
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.todo',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.autosummary'
+    "sphinx.ext.todo",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autosummary",
 ]
 
 napoleon_google_docstring = True
 napoleon_numpy_docstring = False
 
-autodoc_mock_imports = ['numpy', 'matplotlib', 'scipy', 'shapely',
-                        'networkx', 'tqdm', 'mpl_toolkits']
+autodoc_mock_imports = [
+    "numpy",
+    "matplotlib",
+    "scipy",
+    "shapely",
+    "networkx",
+    "tqdm",
+    "mpl_toolkits",
+]
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'pypsbuilder'
-copyright = '2020, Ondrej Lexa'
-author = 'Ondrej Lexa'
+project = "pypsbuilder"
+copyright = "2020, Ondrej Lexa"
+author = "Ondrej Lexa"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '2.3'
+version = "2.4"
 # The full version, including alpha/beta/rc tags.
-release = '2.3.6'
+release = "2.4.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -82,22 +89,21 @@ language = None
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', '**.ipynb_checkpoints', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "**.ipynb_checkpoints", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = True
 
-autodoc_default_options = {'member-order': 'bysource',
-                           'show-inheritance': True}
+autodoc_default_options = {"member-order": "bysource", "show-inheritance": True}
 autosummary_generate = True
 # -- Options for HTML output ----------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -108,7 +114,7 @@ html_theme = 'sphinx_rtd_theme'
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Hide source link
 html_show_sourcelink = False
@@ -116,7 +122,7 @@ html_show_sourcelink = False
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'pypsbuilderdoc'
+htmlhelp_basename = "pypsbuilderdoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -125,15 +131,12 @@ latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -143,8 +146,13 @@ latex_elements = {
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'pypsbuilder.tex', 'pypsbuilder Documentation',
-     'Ondrej Lexa', 'manual'),
+    (
+        master_doc,
+        "pypsbuilder.tex",
+        "pypsbuilder Documentation",
+        "Ondrej Lexa",
+        "manual",
+    ),
 ]
 
 
@@ -152,10 +160,7 @@ latex_documents = [
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'pypsbuilder', 'pypsbuilder Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "pypsbuilder", "pypsbuilder Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -164,7 +169,13 @@ man_pages = [
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'pypsbuilder', 'pypsbuilder Documentation',
-     author, 'pypsbuilder', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "pypsbuilder",
+        "pypsbuilder Documentation",
+        author,
+        "pypsbuilder",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]

{pypsbuilder-2.3.6 → pypsbuilder-2.4.0}/pypsbuilder/__init__.py

@@ -22,7 +22,7 @@ __all__ = (
     "get_tcapi",
 )
 
-__version__ = "2.3.6"
+__version__ = "2.4.0"
 __author__ = "Ondrej Lexa"
 __copyright__ = "© Ondrej Lexa 2023"
 __email__ = "lexa.ondrej@gmail.com"

{pypsbuilder-2.3.6 → pypsbuilder-2.4.0}/pypsbuilder/psexplorer.py

@@ -46,7 +46,7 @@ from matplotlib import ticker
 
 from shapely.geometry import MultiPoint, Point, LineString
 from shapely.ops import linemerge
-from scipy.interpolate import Rbf, interp1d
+from scipy.interpolate import Rbf, interp1d, SmoothBivariateSpline
 from scipy.linalg import LinAlgWarning, lstsq
 from scipy.interpolate import griddata  # interp2d
 from tqdm import tqdm, trange
@@ -539,17 +539,18 @@ class PS:
         if self.gridded:
             for ix, grid in self.grids.items():
                 if key in grid.masks:
-                    results = grid.gridcalcs[grid.masks[key] & (grid.status == 1)]
+                    ok = grid.masks[key] & (grid.status == 1)
+                    results = grid.gridcalcs[ok]
                     if len(results) > 0:
                         if phase in results[0].phases:
                             gdt = zip(
-                                grid.xg[grid.masks[key]],
-                                grid.yg[grid.masks[key]],
+                                grid.xg[ok],
+                                grid.yg[ok],
                                 results,
-                                grid.status[grid.masks[key]],
+                                grid.status[ok],
                             )
-                            for x, y, res, ok in gdt:
-                                if ok == 1:
+                            for x, y, res, status in gdt:
+                                if status == 1:
                                     dt["pts"].append((x, y))
                                     dt["data"].append(eval_expr(expr, res[phase]))
         # else:
@@ -912,12 +913,15 @@ class PS:
         """
         if self.check_phase_expr(phase, expr):
             dt = self.collect_data(key, phase, expr, which=which)
-            x, y = np.array(dt["pts"]).T
-            fig, ax = plt.subplots()
-            pts = ax.scatter(x, y, c=dt["data"])
-            ax.set_title("{} - {}({})".format(" ".join(key), phase, expr))
-            plt.colorbar(pts)
-            plt.show()
+            if dt["pts"]:
+                x, y = np.array(dt["pts"]).T
+                fig, ax = plt.subplots()
+                pts = ax.scatter(x, y, c=dt["data"])
+                ax.set_title("{} - {}({})".format(" ".join(key), phase, expr))
+                plt.colorbar(pts)
+                plt.show()
+            else:
+                print("No data collected")
 
     def show_grid(
         self, phase, expr=None, interpolation=None, label=False, skiplabels=0, labelfs=6
@@ -991,6 +995,8 @@ class PS:
         fig=None,
         fig_kw={},
         isopleths=False,
+        which=7,
+        smooth=0,
     ):
         """Function to plot root squared error of calculated and estimated values.
 
@@ -1013,6 +1019,9 @@ class PS:
                 Default None
             fig_kw: dict passed to subplots method.
             isopleths (bool): When True, searched isoplots are shown.Default False
+            which (int): Bitopt defining from where data are collected. 0 bit -
+                invariant points, 1 bit - uniariant lines and 2 bit - GridData
+                points
 
         Example:
             >>> pt.search_composition(
@@ -1027,16 +1036,25 @@ class PS:
                 err = []
                 for phase, expr, val in zip(args[::3], args[1::3], args[2::3]):
                     if self.check_phase_expr(phase, expr):
-                        err.append((self.get_gridded(phase, expr) - val) ** 2)
+                        err.append(
+                            (
+                                self.get_gridded(
+                                    phase, expr, which=which, smooth=smooth
+                                )
+                                - val
+                            )
+                            ** 2
+                        )
 
-                err = np.sqrt(sum(err))
+                err = np.sqrt(sum(err)) / len(err)
                 r, c = np.unravel_index(np.nanargmin(err), err.shape)
                 p = self.yspace[r]
                 T = self.xspace[c]
+                minerr = err[r, c]
                 if geterror:
                     return err
                 elif getpt:
-                    return p, T, np.nanmin(err)
+                    return p, T, minerr
                 else:
                     if fig is None:
                         fig, ax = plt.subplots(**fig_kw)
@@ -1064,7 +1082,7 @@ class PS:
                     ax.set_ylim(self.yrange)
                     fig.colorbar(im)
 
-                    ax.set_title(f"RMSE - Min at {T} {p}")
+                    ax.set_title(f"RMSE - MinErr={minerr:g} at {T} {p}")
                     fig.tight_layout()
                     plt.show()
             else:
@@ -1245,6 +1263,38 @@ class PS:
                 print(output)
                 return res[0]
 
+    def remove_grid_data(self, key, phase, expr):
+        """Remove calculated data from grid and mark as failed
+
+        Note: Click on all data to be discarded by mouse and finish be Enter
+
+        Args:
+            key (frozenset): Key identifying divariant field
+            phase (str): Phase or end-member named
+            expr (str): Expression to evaluate. It could use any variable
+                existing for given phase. Check `all_data_keys` property for
+                possible variables.
+        """
+
+        if self.gridded:
+            dt = self.collect_data(key, phase, expr, which=4)
+            x, y = np.array(dt["pts"]).T
+            fig, ax = plt.subplots()
+            pts = ax.scatter(x, y, c=dt["data"])
+            plt.colorbar(pts)
+            xy = plt.ginput(0)
+            plt.close(fig)
+            for x, y in xy:
+                ix = self.get_section_id(x, y)
+                if ix is not None:
+                    r, c = self.grids[ix].get_indexes(x, y)
+                    self.grids[ix].status[r, c] = 0
+                    # self.grids[ix].masks[key][r, c] = False
+                    self.grids[ix].gridcalcs[r, c] = None
+                    self.grids[ix].delta[r, c] = np.nan
+        else:
+            print("Not yet gridded...")
+
     def ginput_path(self, label=False, skiplabels=0, labelfs=6):
         """Collect Path data by mouse digitizing.
 
@@ -1293,7 +1343,8 @@ class PS:
                 invariant points, 1 bit - uniariant lines and 2 bit - GridData
                 points. Default 7 (all data)
             method: Interpolation method. Default is 'rbf', other option is
-                'quadratic', which uses least-square fit to quadratic surface.
+                'quadratic', which uses least-square fit to quadratic surface
+                or 'spline' for bivariate spline interpolation.
             rbf_func: Default 'thin_plate'. See scipy.interpolation.Rbf
             smooth (int): Values greater than zero increase the smoothness
                 of the approximation. 0 is for interpolation (default),
@@ -1301,7 +1352,9 @@ class PS:
             epsilon (int): Adjustable constant for gaussian or multiquadrics
                 functions - defaults to approximate average distance between
                 nodes (which is a good start).
+            degree (int): Degrees of the bivariate spline. Default is 3.
             refine (int): Degree of grid refinement. Default 1
+            filter_outliers (bool): Whether to filter outliers. Defaut False.
             filled (bool): Whether to contours should be filled. Defaut True.
             filled_over (bool): Whether to overlay contourline over filled
                 contours. Defaut False.
@@ -1346,6 +1399,8 @@ class PS:
             gradient = kwargs.get("gradient", False)
             dx = kwargs.get("dx", True)
             only = kwargs.get("only", None)
+            filter_outliers = kwargs.get("only", False)
+            degree = kwargs.get("degree", 3)
             refine = kwargs.get("refine", 1)
             method = kwargs.get("method", "rbf")
             rbf_func = kwargs.get("rbf_func", "thin_plate")
@@ -1424,9 +1479,22 @@ class PS:
                         self.gridystep / refine,
                     )
                     tg, pg = np.meshgrid(ttspace, ppspace)
-                    x, y = np.array(recs[key]["pts"]).T
-                    pts = recs[key]["pts"]
-                    data = recs[key]["data"]
+                    pts = np.array(recs[key]["pts"])
+                    x, y = pts.T
+                    data = np.array(recs[key]["data"])
+                    # filter outliers
+                    if filter_outliers:
+                        A = np.c_[np.ones_like(x), x, y, x * y, x**2, y**2]
+                        C, _, _, _ = lstsq(A, data)
+                        # evaluate it on a grid
+                        vals = np.dot(
+                            np.c_[np.ones_like(x), x, y, x * y, x**2, y**2], C
+                        )
+                        err = abs(vals - data)
+                        ok = err < err.std()
+                        pts = pts[ok, :]
+                        x, y = pts.T
+                        data = data[ok]
                     try:
                         if method == "quadratic":
                             tgg = tg.flatten()
@@ -1445,6 +1513,11 @@ class PS:
                                 ],
                                 C,
                             ).reshape(tg.shape)
+                        elif method == "spline":
+                            interp = SmoothBivariateSpline(
+                                x, self.ratio * y, data, kx=degree, ky=degree
+                            )
+                            zg = interp(tg, self.ratio * pg)
                         else:
                             with warnings.catch_warnings():
                                 warnings.filterwarnings("error")
@@ -1461,29 +1534,19 @@ class PS:
                         if self.show_errors:
                             print(e)
                         try:
-                            if method == "quadratic":
-                                print(
-                                    "Using nearest method in {}".format(
-                                        " ".join(sorted(list(key)))
-                                    )
-                                )
-                                zg = griddata(
-                                    np.array(pts),
-                                    data,
-                                    (tg, pg),
-                                    method="nearest",
-                                    rescale=True,
-                                )
-                            else:
-                                # preprocess with griddata
-                                zg_tmp = griddata(
-                                    pts, data, (tg, pg), method="linear", rescale=True
-                                )
+                            zg = griddata(
+                                np.array(pts),
+                                data,
+                                (tg, pg),
+                                method="nearest",
+                                rescale=True,
+                            )
+                            if method == "rbf":
                                 # locate valid data
-                                ri, ci = np.nonzero(np.isfinite(zg_tmp))
+                                ri, ci = np.nonzero(np.isfinite(zg))
                                 x, y, z = np.array(
                                     [
-                                        [tg[r, c], pg[r, c], zg_tmp[r, c]]
+                                        [tg[r, c], pg[r, c], zg[r, c]]
                                         for r, c in zip(ri, ci)
                                     ]
                                 ).T
@@ -1501,19 +1564,25 @@ class PS:
                                         epsilon=epsilon,
                                     )
                                     zg = rbf(tg, self.ratio * pg)
+                            if method == "spline":
+                                # locate valid data
+                                ri, ci = np.nonzero(np.isfinite(zg))
+                                x, y, z = np.array(
+                                    [
+                                        [tg[r, c], pg[r, c], zg[r, c]]
+                                        for r, c in zip(ri, ci)
+                                    ]
+                                ).T
+                                interp = SmoothBivariateSpline(
+                                    x, self.ratio * y, z, kx=degree, ky=degree
+                                )
+                                zg = interp(tg, self.ratio * pg)
                         except Exception:
                             print(
                                 "Using nearest method in {}".format(
                                     " ".join(sorted(list(key)))
                                 )
                             )
-                            zg = griddata(
-                                np.array(pts),
-                                data,
-                                (tg, pg),
-                                method="nearest",
-                                rescale=True,
-                            )
                     # experimental
                     if gradient:
                         grd = np.gradient(zg, self.gridxstep, self.gridystep)
@@ -1674,6 +1743,9 @@ class PS:
             epsilon (int): Adjustable constant for gaussian or multiquadrics
                 functions - defaults to approximate average distance between
                 nodes (which is a good start).
+            degree (int): Degrees of the bivariate spline. Default is 3.
+            refine (int): Degree of grid refinement. Default 1
+            filter_outliers (bool): Whether to filter outliers. Defaut False.
             out (str or list): Highligt zero-mode lines for given phases.
             overlay (bool): Whether to show assemblage fields. Default True
             high (frozenset or list): Highlight divariant fields identified
@@ -1707,6 +1779,8 @@ class PS:
             cdf = kwargs.get("cdf", False)
             overlay = kwargs.get("overlay", True)
             only = kwargs.get("only", None)
+            filter_outliers = kwargs.get("only", False)
+            degree = kwargs.get("degree", 3)
             refine = kwargs.get("refine", 1)
             method = kwargs.get("method", "rbf")
             rbf_func = kwargs.get("rbf_func", "thin_plate")
@@ -1782,6 +1856,19 @@ class PS:
                     x, y = np.array(recs[key]["pts"]).T
                     pts = recs[key]["pts"]
                     data = recs[key]["data"]
+                    # filter outliers
+                    if filter_outliers:
+                        A = np.c_[np.ones_like(x), x, y, x * y, x**2, y**2]
+                        C, _, _, _ = lstsq(A, data)
+                        # evaluate it on a grid
+                        vals = np.dot(
+                            np.c_[np.ones_like(x), x, y, x * y, x**2, y**2], C
+                        )
+                        err = abs(vals - data)
+                        ok = err < err.std()
+                        pts = pts[ok, :]
+                        x, y = pts.T
+                        data = data[ok]
                     try:
                         if method == "quadratic":
                             tgg = tg.flatten()
@@ -1800,22 +1887,76 @@ class PS:
                                 ],
                                 C,
                             ).reshape(tg.shape)
-                        else:
-                            rbf = Rbf(
-                                x,
-                                self.ratio * y,
-                                data,
-                                function=rbf_func,
-                                smooth=smooth,
-                                epsilon=epsilon,
+                        elif method == "spline":
+                            interp = SmoothBivariateSpline(
+                                x, self.ratio * y, data, kx=degree, ky=degree
                             )
-                            zg = rbf(tg, self.ratio * pg)
+                            zg = interp(tg, self.ratio * pg)
+                        else:
+                            with warnings.catch_warnings():
+                                warnings.filterwarnings("error")
+                                rbf = Rbf(
+                                    x,
+                                    self.ratio * y,
+                                    data,
+                                    function=rbf_func,
+                                    smooth=smooth,
+                                    epsilon=epsilon,
+                                )
+                                zg = rbf(tg, self.ratio * pg)
                     except Exception as e:
                         if self.show_errors:
                             print(e)
-                        zg = griddata(
-                            np.array(pts), data, (tg, pg), method="cubic", rescale=True
-                        )
+                        try:
+                            zg = griddata(
+                                np.array(pts),
+                                data,
+                                (tg, pg),
+                                method="nearest",
+                                rescale=True,
+                            )
+                            if method == "rbf":
+                                # locate valid data
+                                ri, ci = np.nonzero(np.isfinite(zg))
+                                x, y, z = np.array(
+                                    [
+                                        [tg[r, c], pg[r, c], zg[r, c]]
+                                        for r, c in zip(ri, ci)
+                                    ]
+                                ).T
+                                # do Rbf extrapolation
+                                with warnings.catch_warnings():
+                                    warnings.filterwarnings(
+                                        "ignore", category=LinAlgWarning
+                                    )
+                                    rbf = Rbf(
+                                        x,
+                                        self.ratio * y,
+                                        z,
+                                        function=rbf_func,
+                                        smooth=smooth,
+                                        epsilon=epsilon,
+                                    )
+                                    zg = rbf(tg, self.ratio * pg)
+                            if method == "spline":
+                                # locate valid data
+                                ri, ci = np.nonzero(np.isfinite(zg))
+                                x, y, z = np.array(
+                                    [
+                                        [tg[r, c], pg[r, c], zg[r, c]]
+                                        for r, c in zip(ri, ci)
+                                    ]
+                                ).T
+                                interp = SmoothBivariateSpline(
+                                    x, self.ratio * y, z, kx=degree, ky=degree
+                                )
+                                zg = interp(tg, self.ratio * pg)
+                        except Exception:
+                            print(
+                                "Using nearest method in {}".format(
+                                    " ".join(sorted(list(key)))
+                                )
+                            )
                     # ------------
                     scx = (tmax - tmin + 2 * self.gridxstep) / zg.shape[1]
                     scy = (pmax - pmin + 2 * self.gridystep) / zg.shape[0]
@@ -2123,15 +2264,18 @@ class PS:
                     tg, pg = self.xg[slc], self.yg[slc]
                     x, y = np.array(recs[key]["pts"]).T
                     # Use scaling
-                    rbf = Rbf(
-                        x,
-                        self.ratio * y,
-                        recs[key]["data"],
-                        function="linear",
-                        smooth=smooth,
-                    )
-                    zg = rbf(tg, self.ratio * pg)
-                    gd[self.masks[key]] = zg[self.masks[key][slc]]
+                    try:
+                        rbf = Rbf(
+                            x,
+                            self.ratio * y,
+                            recs[key]["data"],
+                            function="linear",
+                            smooth=smooth,
+                        )
+                        zg = rbf(tg, self.ratio * pg)
+                        gd[self.masks[key]] = zg[self.masks[key][slc]]
+                    except Exception:
+                        pass  # pass silently
                 return gd
         else:
             print("Not yet gridded...")
@@ -2364,7 +2508,7 @@ class PTPS(PS):
                 t, p = splt(step), splp(step)
                 key = self.identify(t, p)
                 ix = self.get_section_id(t, p)
-                if ix is not None:
+                if (ix is not None) and (key is not None):
                     r, c = self.grids[ix].get_indexes(t, p)
                     calc = None
                     if self.grids[ix].status[r, c] == 1:
@@ -2385,6 +2529,8 @@ class PTPS(PS):
                             results.append(res[0])
                     else:
                         err += 1
+                else:
+                    err += 1
             if err > 0:
                 print("Solution not found on {} points".format(err))
             return PTpath(points, results)
@@ -2888,8 +3034,10 @@ class GridData:
             y (float): y-coordiante of point
 
         """
-        c = np.searchsorted(self.xspace, x)
-        r = np.searchsorted(self.yspace, y)
+        # c = np.searchsorted(self.xspace, x)
+        c = np.argmin((self.xspace - x) ** 2)
+        # r = np.searchsorted(self.yspace, y)
+        r = np.argmin((self.yspace - y) ** 2)
         return r, c
 
     def contains(self, x, y):

{pypsbuilder-2.3.6 → pypsbuilder-2.4.0}/pypsbuilder.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pypsbuilder
-Version: 2.3.6
+Version: 2.4.0
 Summary: THERMOCALC front-end for constructing and analyzing PT pseudosections
 Home-page: https://github.com/ondrolexa/pypsbuilder
 Author: Ondrej Lexa
@@ -88,6 +88,12 @@ pypsbuilder is free software: you can redistribute it and/or modify it under the
 # Changelog
 All notable pypsbuilder changes.
 
+## [2.4.0] - 2023-12-21
+### Fixed
+ - important collect_grid_data bug causing isopleths twisting fixed. 
+ - collect_ptpath missing field check added
+ - remove_grid_data method added
+ - isopleths bivariate spline method added
 ## [2.3.6] - 2023-12-13
 ### Added
  - search_composition method added to PTPS to find best estimate for isopleths intersection

{pypsbuilder-2.3.6 → pypsbuilder-2.4.0}/setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.3.6
+current_version = 2.4.0
 commit = True
 tag = False
 

{pypsbuilder-2.3.6 → pypsbuilder-2.4.0}/setup.py

@@ -5,34 +5,27 @@ from setuptools import setup, find_packages
 
 CURRENT_PATH = path.abspath(path.dirname(__file__))
 
-with open(path.join(CURRENT_PATH, 'README.md')) as readme_file:
+with open(path.join(CURRENT_PATH, "README.md")) as readme_file:
     readme = readme_file.read()
 
-with open(path.join(CURRENT_PATH, 'CHANGELOG.md')) as changelog_file:
+with open(path.join(CURRENT_PATH, "CHANGELOG.md")) as changelog_file:
     changelog = changelog_file.read()
 
-requirements = [
-    'numpy',
-    'matplotlib>=3',
-    'scipy',
-    'networkx',
-    'shapely>=2',
-    'tqdm'
-]
+requirements = ["numpy", "matplotlib>=3", "scipy", "networkx", "shapely>=2", "tqdm"]
 
 setup(
-    name='pypsbuilder',
-    version='2.3.6',
+    name="pypsbuilder",
+    version="2.4.0",
     description="THERMOCALC front-end for constructing and analyzing PT pseudosections",
-    long_description=readme + '\n\n' + changelog,
+    long_description=readme + "\n\n" + changelog,
     long_description_content_type="text/markdown",
     author="Ondrej Lexa",
-    author_email='lexa.ondrej@gmail.com',
-    url='https://github.com/ondrolexa/pypsbuilder',
+    author_email="lexa.ondrej@gmail.com",
+    url="https://github.com/ondrolexa/pypsbuilder",
     license="MIT",
     python_requires=">=3.8",
     packages=find_packages(),
-    package_data={'pypsbuilder.images': ['*.png']},
+    package_data={"pypsbuilder.images": ["*.png"]},
     entry_points="""
     [console_scripts]
     ptbuilder=pypsbuilder.psbuilders:ptbuilder
@@ -46,13 +39,13 @@ setup(
     """,
     install_requires=requirements,
     zip_safe=False,
-    keywords='pypsbuilder',
+    keywords="pypsbuilder",
     classifiers=[
-        'Development Status :: 4 - Beta',
-        'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
-        'Programming Language :: Python :: 3 :: Only',
-        'Topic :: Scientific/Engineering',
-        'Topic :: Utilities'
-    ]
+        "Development Status :: 4 - Beta",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+        "Programming Language :: Python :: 3 :: Only",
+        "Topic :: Scientific/Engineering",
+        "Topic :: Utilities",
+    ],
 )