Various code cleanups

Author: gb119

Stoner/Analysis.py

@@ -384,23 +384,21 @@ def stitch(self, other, xcol=None, ycol=None, overlap=None, min_overlap=0.0, mod
         otherpoints = other.column([_.xcol, _.ycol])
         otherpoints = otherpoints[otherpoints[:, 0].argsort(), :]
         self_second = np.max(points[:, 0]) > np.max(otherpoints[:, 0])
-        if overlap is None:  # Calculate the overlap
-            lower = max(np.min(points[:, 0]), np.min(otherpoints[:, 0]))
-            upper = min(np.max(points[:, 0]), np.max(otherpoints[:, 0]))
-        elif isinstance(overlap, int) and overlap > 0:
-            if self_second:
-                lower = points[0, 0]
-                upper = points[overlap, 0]
-            else:
-                lower = points[-overlap - 1, 0]
-                upper = points[-1, 0]
-        elif (
-            isinstance(overlap, tuple)
-            and len(overlap) == 2
-            and isinstance(overlap[0], float and isinstance(overlap[1], float))
-        ):
-            lower = min(overlap)
-            upper = max(overlap)
+        match overlap:
+            case int() if overlap > 0:
+                if self_second:
+                    lower = points[0, 0]
+                    upper = points[overlap, 0]
+                else:
+                    lower = points[-overlap - 1, 0]
+                    upper = points[-1, 0]
+            case (float(), float()):
+                lower = min(overlap)
+                upper = max(overlap)
+            case _:
+                lower = max(np.min(points[:, 0]), np.min(otherpoints[:, 0]))
+                upper = min(np.max(points[:, 0]), np.max(otherpoints[:, 0]))
+
         inrange = np.logical_and(points[:, 0] >= lower, points[:, 0] <= upper)
         points = points[inrange]
         num_pts = points.shape[0]

Stoner/Core.py

@@ -658,6 +658,7 @@ def _load(self, filename, *args, **kargs):
             datafile.seek(0)
             reader = csv.reader(datafile, dialect=tab_delimited())
             cols = 0
+            max_rows = 0
             for ix, metadata in enumerate(reader):
                 if ix == 0:
                     row = metadata

Stoner/HDF5.py

@@ -24,6 +24,7 @@
 from .folders import DataFolder
 from .Image.core import ImageFile, ImageArray
 from .core.utils import copy_into
+from .tools.file import HDFFileManager
 
 
 def get_hdf_loader(f, default_loader=lambda *args, **kargs: None):
@@ -52,68 +53,6 @@ def get_hdf_loader(f, default_loader=lambda *args, **kargs: None):
     return getattr(globals()[typ], "read_hdf5", default_loader)
 
 
-class HDFFileManager:
-    """Context manager for HDF5 files."""
-
-    def __init__(self, filename, mode="r"):
-        """Initialise context handler.
-
-        Works out the filename and group in cases the input flename includes a path to a sub group.
-
-        Checks the file is actually an h4py file that is openable with the given mode.
-        """
-        self.mode = mode
-        self.handle = None
-        self.file = None
-        self.close = True
-        self.group = ""
-        # Handle the case we're passed an already open h5py object
-        if not isinstance(filename, path_types) or mode == "w":  # passed an already open h5py object
-            self.filename = filename
-            return
-        # Here we deal with a string or path filename
-        parts = str(filename).split(os.path.sep)
-        bits = len(parts)
-        for ix in range(bits):
-            testname = "/".join(parts[: bits - ix])
-            if path.exists(testname):
-                filename = testname
-                break
-
-        try:
-            if not mode.startswith("w"):
-                with h5py.File(filename, "r"):
-                    pass
-        except (IOError, OSError) as err:
-            raise StonerLoadError(f"{filename} not at HDF5 File") from err
-        self.filename = filename
-
-    def __enter__(self):
-        """Open the hdf file with given mode and navigate to the group."""
-        if isinstance(self.filename, (h5py.File, h5py.Group)):  # passed an already open h5py object
-            self.handle = self.filename
-            if isinstance(self.filename, h5py.Group):
-                self.file = self.filename.file
-            else:
-                self.file = self.filename
-            self.close = False
-        elif isinstance(self.filename, path_types):  # Passed something to open
-            handle = h5py.File(self.filename, self.mode)
-            self.file = handle
-            for grp in self.group.split("/"):
-                if grp.strip() != "":
-                    handle = handle[grp]
-            self.handle = handle
-        else:
-            raise StonerLoadError("Note a resource that can be handled with HDF")
-        return self.handle
-
-    def __exit__(self, _type, _value, _traceback):
-        """Ensure we close the hdf file no matter what."""
-        if self.file is not None and self.close:
-            self.file.close()
-
-
 class HDF5File(DataFile):
     """A sub class of DataFile that sores itself in a HDF5File or group.
 

Stoner/Zip.py

@@ -282,7 +282,7 @@ def _dialog(self, mode="r"):
 
         if mode == "r":
             what = "file"
-        elif mode == "w":
+        else:
             what = "save"
 
         dlg = get_filedialog(what=what, filetypes=file_wildcard)

Stoner/analysis/fitting/mixins.py

@@ -1451,7 +1451,7 @@ def lmfit(self, model, xcol=None, ycol=None, p0=None, sigma=None, **kargs):
                 ret.column_headers = []
                 ret.setas = ""
                 prefix = ret["lmfit.prefix"][-1]
-                ix = 0
+                ix = fixed = 0
                 for ix, p in enumerate(model.param_names):
                     label = self.metadata.get(f"{prefix}{p} label", p)
                     units = self.metadata.get(f"{prefix}{p} units", "")

Stoner/formats/data/generic.py

@@ -121,6 +121,7 @@ def load_tdi_format(new_data, filename, *args, **kargs):
         datafile.seek(0)
         reader = csv.reader(datafile, dialect=tab_delimited())
         cols = 0
+        max_rows = 0
         for ix, metadata in enumerate(reader):
             if ix == 0:
                 row = metadata

Stoner/formats/data/rigs.py

@@ -191,6 +191,7 @@ def _sa_cmd(new_data, parts):
 def load_easyplot(new_data, filename, *args, **kargs):
     """Private loader method."""
     new_data.filename = filename
+    delimiter = kargs.pop("delimiter")
 
     datastart = -1
     dataend = -1
@@ -257,6 +258,7 @@ def load_pinklib(new_data, filename=None, *args, **kargs):
         new_data.get_filename("r")
     else:
         new_data.filename = filename
+    header_line = 0
     with FileManager(new_data.filename, "r", errors="ignore", encoding="utf-8") as f:  # Read filename linewise
         if "PINKlibrary" not in f.readline():
             raise StonerLoadError("Not a PINK file")

Stoner/formats/rigs.py

@@ -214,6 +214,7 @@ def _load(self, filename, *args, **kargs):
 
         datastart = -1
         dataend = -1
+        delimiter = kargs.pop("delimiter", None)
 
         i = 0
         with FileManager(self.filename, "r", errors="ignore", encoding="utf-8") as data:

Stoner/plot/core.py

@@ -1003,6 +1003,8 @@ def image_plot(self, xcol=None, ycol=None, zcol=None, shape=None, xlim=None, yli
             cmap = colormaps[kargs["cmap"]]
         elif "cmap" in nonkargs and isinstance(kargs["cmap"], str):
             cmap = colormaps(nonkargs["cmap"])
+        else:
+            cmap = colormaps["viridis"]
         if Z.ndim == 2:
             Z = cmap(Z)
         elif Z.ndim != 3:

Stoner/tools/file.py

@@ -8,6 +8,8 @@
 from traceback import format_exc
 from typing import Union, Sequence, Dict, Type, Tuple, Optional
 
+import h5py
+
 from ..compat import string_types, path_types, bytes2str, str2bytes
 from .widgets import fileDialog
 from .classes import subclasses
@@ -284,3 +286,65 @@ def __enter__(self):
         else:
             length = len(self.file)
         return self.file, length
+
+
+class HDFFileManager:
+    """Context manager for HDF5 files."""
+
+    def __init__(self, filename, mode="r"):
+        """Initialise context handler.
+
+        Works out the filename and group in cases the input flename includes a path to a sub group.
+
+        Checks the file is actually an h4py file that is openable with the given mode.
+        """
+        self.mode = mode
+        self.handle = None
+        self.file = None
+        self.close = True
+        self.group = ""
+        # Handle the case we're passed an already open h5py object
+        if not isinstance(filename, path_types) or mode == "w":  # passed an already open h5py object
+            self.filename = filename
+            return
+        # Here we deal with a string or path filename
+        parts = str(filename).split(os.path.sep)
+        bits = len(parts)
+        for ix in range(bits):
+            testname = "/".join(parts[: bits - ix])
+            if os.path.exists(testname):
+                filename = testname
+                break
+
+        try:
+            if not mode.startswith("w"):
+                with h5py.File(filename, "r"):
+                    pass
+        except (IOError, OSError) as err:
+            raise StonerLoadError(f"{filename} not at HDF5 File") from err
+        self.filename = filename
+
+    def __enter__(self):
+        """Open the hdf file with given mode and navigate to the group."""
+        if isinstance(self.filename, (h5py.File, h5py.Group)):  # passed an already open h5py object
+            self.handle = self.filename
+            if isinstance(self.filename, h5py.Group):
+                self.file = self.filename.file
+            else:
+                self.file = self.filename
+            self.close = False
+        elif isinstance(self.filename, path_types):  # Passed something to open
+            handle = h5py.File(self.filename, self.mode)
+            self.file = handle
+            for grp in self.group.split("/"):
+                if grp.strip() != "":
+                    handle = handle[grp]
+            self.handle = handle
+        else:
+            raise StonerLoadError("Note a resource that can be handled with HDF")
+        return self.handle
+
+    def __exit__(self, _type, _value, _traceback):
+        """Ensure we close the hdf file no matter what."""
+        if self.file is not None and self.close:
+            self.file.close()