ref: rename IndentationDataSet to IndentationGroup to avoid ambiguities

.gitignore

@@ -105,3 +105,4 @@ venv.bak/
 
 *.c
 _version_save.py
+*.bib.bak

docs/sec_code_reference.rst

@@ -18,9 +18,9 @@ at the module level.
 
     alias of :class:`nanite.indent.Indentation`
 
-.. class:: nanite.IndentationDataSet
+.. class:: nanite.IndentationGroup
 
-    alias of :class:`nanite.dataset.IndentationDataSet`
+    alias of :class:`nanite.group.IndentationGroup`
 
 .. class:: nanite.IndentationRater
 
@@ -41,12 +41,12 @@ Force-indentation data
    :undoc-members:
 
 
-.. _sec_ref_dataset:
+.. _sec_ref_group:
 
-Datasets
-========
+Groups
+======
 
-.. automodule:: nanite.dataset
+.. automodule:: nanite.group
    :members:
    :undoc-members:
 

nanite/__init__.py

@@ -1,4 +1,4 @@
-from .dataset import IndentationDataSet  # noqa: F401
+from .group import IndentationGroup  # noqa: F401
 from . import fit  # noqa: F401
 from .indent import Indentation, type_indentation  # noqa: F401
 from . import model  # noqa: F401

nanite/cli/rating.py

@@ -13,7 +13,7 @@
 import tifffile
 
 from ..indent import Indentation
-from ..dataset import IndentationDataSet
+from ..group import IndentationGroup
 from ..read import get_data_paths, get_data_paths_enum
 from ..rate import io as rio
 
@@ -186,8 +186,8 @@ def fit():
             ptsv.open(mode="a") as ts:
         for pp in datapaths:
             print("Processing: {}".format(pp))
-            ds = IndentationDataSet(pp)
-            for idnt in ds:
+            grp = IndentationGroup(pp)
+            for idnt in grp:
                 fit_data(idnt)
                 # save statistics
                 stats = [str(dd[1](idnt)) for dd in dlist]
@@ -211,7 +211,7 @@ def fit_data(path, enum=0, profile_path=PROFILE_PATH):
     if isinstance(path, Indentation):
         idnt = path
     else:
-        idnt = IndentationDataSet(path)[enum]
+        idnt = IndentationGroup(path)[enum]
 
     pf = Profile(path=profile_path, create=False)
 

nanite/dataset.py → nanite/group.py

@@ -4,9 +4,9 @@
 from .indent import Indentation, type_indentation
 
 
-class IndentationDataSet(object):
+class IndentationGroup(object):
     def __init__(self, path=None, callback=None):
-        """Collection of Indentation
+        """Group of Indentation
 
         Parameters
         ----------
@@ -34,7 +34,7 @@ def __init__(self, path=None, callback=None):
                                             ))
 
     def __add__(self, ds):
-        out = IndentationDataSet()
+        out = IndentationGroup()
         out._mmlist = self._mmlist + ds._mmlist
         return out
 
@@ -52,18 +52,18 @@ def __len__(self):
         return len(self._mmlist)
 
     def __repr__(self):
-        return "IndentationDataSet: {} ".format(self._mmlist.__repr__())
+        return "IndentationGroup: {} ".format(self._mmlist.__repr__())
 
     def append(self, item):
         self._mmlist.append(item)
 
     def index(self, item):
         return self._mmlist.index(item)
 
-    def subset_with_path(self, path):
-        """Return a subset with measurements matching `path`"""
-        subset = IndentationDataSet()
+    def subgroup_with_path(self, path):
+        """Return a subgroup with measurements matching `path`"""
+        subgroup = IndentationGroup()
         for idnt in self:
             if pathlib.Path(idnt.path) == pathlib.Path(path):
-                subset.append(idnt)
-        return subset
+                subgroup.append(idnt)
+        return subgroup

nanite/qmap.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 
-from .dataset import IndentationDataSet
+from .group import IndentationGroup
 
 
 class DataMissingWarning(UserWarning):
@@ -16,20 +16,20 @@ def __init__(self, path_or_dataset, callback=None):
 
         Parameters
         ----------
-        path_or_dataset: str or nanite.IndentationDataSet
+        path_or_dataset: str or nanite.IndentationGroup
             The path to the data file. The data format is determined
             using the extension of the file and the data is loaded
             with the correct method.
         callback: callable or None
             A method that accepts a float between 0 and 1
             to externally track the process of loading the data.
         """
-        if isinstance(path_or_dataset, IndentationDataSet):
-            ds = path_or_dataset
+        if isinstance(path_or_dataset, IndentationGroup):
+            group = path_or_dataset
         else:
-            ds = IndentationDataSet(path=path_or_dataset, callback=callback)
-        #: Experimental dataset
-        self.ds = ds
+            group = IndentationGroup(path=path_or_dataset, callback=callback)
+        #: Indentation data (instance of :class:`nanite.IndentationGroup`)
+        self.group = group
 
         # Feature functions
         self._feature_funcs = {
@@ -98,7 +98,7 @@ def _map_grid(self, coords, map_data):
     @functools.lru_cache(maxsize=32)
     def extent(self):
         """extent (x1, x2, y1, y2) [µm]"""
-        idnt0 = self.ds[0]
+        idnt0 = self.group[0]
         # get extent of the map
         sx = idnt0.metadata["grid size x [µm]"]
         sy = idnt0.metadata["grid size y [µm]"]
@@ -113,7 +113,7 @@ def extent(self):
     @functools.lru_cache(maxsize=32)
     def shape(self):
         """shape of the map [px]"""
-        idnt0 = self.ds[0]
+        idnt0 = self.group[0]
         # get shape of the map
         shape = (idnt0.metadata["grid size x [px]"],
                  idnt0.metadata["grid size y [px]"]
@@ -170,7 +170,7 @@ def get_coords(self, which="px"):
             kx = "position x [µm]"
             ky = "position y [µm]"
         coords = []
-        for idnt in self.ds:
+        for idnt in self.group:
             # We assume that kx and ky are given. This has to be
             # ensured by the file format reader for qmaps.
             cc = [idnt.metadata[kx], idnt.metadata[ky]]
@@ -200,7 +200,7 @@ def get_qmap(self, feature, qmap_only=False):
 
         map_data = []
         ffunc = self._feature_funcs[feature]
-        for idnt in self.ds:
+        for idnt in self.group:
             val = ffunc(idnt)
             map_data.append(val)
 

nanite/rate/io.py

@@ -11,7 +11,7 @@
 import numpy as np
 from sklearn import model_selection
 
-from ..dataset import IndentationDataSet
+from ..group import IndentationGroup
 from . import rater
 
 
@@ -248,7 +248,7 @@ def load_hdf5(path, meta_only=False):
                 name = dkey + "_" + pathlib.Path(dset.attrs["path"]).name
                 dpath = pathlib.Path(tdir) / name
                 dbin.tofile(str(dpath))
-                dataset_dict[dkey] = IndentationDataSet(dpath)
+                dataset_dict[dkey] = IndentationGroup(dpath)
         # load individual curves
         for akey in h5["analysis"]:
             h5gr = h5["analysis"][akey]

tests/test_dataset.py

@@ -1,16 +1,16 @@
 """Test of data set functionalities"""
 import pathlib
 
-from nanite import Indentation, IndentationDataSet
+from nanite import Indentation, IndentationGroup
 
 
 datadir = pathlib.Path(__file__).resolve().parent / "data"
 jpkfile = datadir / "spot3-0192.jpk-force"
 
 
 def test_afm_data_set():
-    ds1 = IndentationDataSet(jpkfile)
-    ds2 = IndentationDataSet(jpkfile)
+    ds1 = IndentationGroup(jpkfile)
+    ds2 = IndentationGroup(jpkfile)
 
     ds3 = ds1 + ds2
     assert len(ds3) == 2

tests/test_fit_emodulus_search.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 
-from nanite import IndentationDataSet
+from nanite import IndentationGroup
 from nanite.fit import FitDataError
 
 
@@ -14,7 +14,7 @@
 
 
 def test_emodulus_search():
-    ds = IndentationDataSet(jpkfile)
+    ds = IndentationGroup(jpkfile)
     ar = ds[0]
     ar.apply_preprocessing(["compute_tip_position",
                             "correct_force_offset",
@@ -65,7 +65,7 @@ def test_cache_emodulus():
     # Check that the fitting procedure does not perform unneccessary
     # double fits and uses the cached variables for emoduli and
     # minimal indentations.
-    ds = IndentationDataSet(jpkfile)
+    ds = IndentationGroup(jpkfile)
     ar = ds[0]
     ar.apply_preprocessing(["compute_tip_position",
                             "correct_force_offset",
@@ -99,7 +99,7 @@ def test_cache_emodulus():
 def test_fit_data_error():
     # a FitDataError is raised when it is not possible to compute an
     # E(delta) curve:
-    ds = IndentationDataSet(badjpk)
+    ds = IndentationGroup(badjpk)
     ar = ds[0]
     ar.apply_preprocessing(["compute_tip_position",
                             "correct_force_offset",

tests/test_fit_hash.py

@@ -3,15 +3,15 @@
 import time
 
 import nanite
-from nanite import IndentationDataSet
+from nanite import IndentationGroup
 
 
 datapath = pathlib.Path(__file__).parent / "data"
 jpkfile = datapath / "spot3-0192.jpk-force"
 
 
 def test_hash_time():
-    ds1 = IndentationDataSet(jpkfile)
+    ds1 = IndentationGroup(jpkfile)
     apret = ds1[0]
     apret.apply_preprocessing(["compute_tip_position"])
 

tests/test_fit_properties.py

@@ -3,7 +3,7 @@
 import pathlib
 
 from nanite.fit import FitProperties, FP_DEFAULT, FitKeyError
-from nanite import IndentationDataSet
+from nanite import IndentationGroup
 from nanite import model
 
 
@@ -34,7 +34,7 @@ def test_fp_reset():
 
 
 def test_with_dataset():
-    ar = IndentationDataSet(jpkfile)[0]
+    ar = IndentationGroup(jpkfile)[0]
     # Initially, fit properties are not set
     assert not ar.fit_properties
     assert isinstance(ar.fit_properties, dict)
@@ -64,7 +64,7 @@ def test_with_dataset():
 
 
 def test_change_model_key():
-    ar = IndentationDataSet(jpkfile)[0]
+    ar = IndentationGroup(jpkfile)[0]
     # Prepprocessing
     ar.apply_preprocessing(["compute_tip_position",
                             "correct_tip_offset",
@@ -91,7 +91,7 @@ def test_wrong_key():
 
 
 def test_wrong_params_initial():
-    ar = IndentationDataSet(jpkfile)[0]
+    ar = IndentationGroup(jpkfile)[0]
     # Prepprocessing
     ar.apply_preprocessing(["compute_tip_position",
                             "correct_tip_offset",

tests/test_indent.py

@@ -13,7 +13,7 @@
 
 
 def test_apply_preprocessing():
-    ds1 = nanite.IndentationDataSet(jpkfile)
+    ds1 = nanite.IndentationGroup(jpkfile)
     idnt = ds1[0]
     # apply preprocessing by manually setting the list
     idnt.preprocessing = ["compute_tip_position"]
@@ -26,7 +26,7 @@ def test_apply_preprocessing_remember_fit_properties():
     if the preprocessing changes. For user convenience,
     nanite remembers it. This is the test
     """
-    ds1 = nanite.IndentationDataSet(jpkfile)
+    ds1 = nanite.IndentationGroup(jpkfile)
     idnt = ds1[0]
     idnt.apply_preprocessing(["compute_tip_position"])
 
@@ -55,7 +55,7 @@ def test_apply_preprocessing_remember_fit_properties():
 
 
 def test_basic():
-    ds1 = nanite.IndentationDataSet(jpkfile)
+    ds1 = nanite.IndentationGroup(jpkfile)
     idnt = ds1[0]
     # tip-sample separation
     idnt.apply_preprocessing(["compute_tip_position"])
@@ -69,7 +69,7 @@ def test_basic():
 
 
 def test_export():
-    ds1 = nanite.IndentationDataSet(jpkfile)
+    ds1 = nanite.IndentationGroup(jpkfile)
     idnt = ds1[0]
     # tip-sample separation
     idnt.apply_preprocessing(["compute_tip_position"])
@@ -93,7 +93,7 @@ def test_export():
 
 
 def test_fitting():
-    ds1 = nanite.IndentationDataSet(jpkfile)
+    ds1 = nanite.IndentationGroup(jpkfile)
     idnt = ds1[0]
     idnt.apply_preprocessing(["compute_tip_position"])
 
@@ -146,7 +146,7 @@ def test_fitting():
 @pytest.mark.filterwarnings('ignore::nanite.fit.FitWarning')
 def test_get_initial_fit_parameters():
     """This is a convenience function"""
-    ds1 = nanite.IndentationDataSet(jpkfile)
+    ds1 = nanite.IndentationGroup(jpkfile)
     idnt = ds1[0]
     # A: sanity check
     try:
@@ -179,7 +179,7 @@ def test_get_model():
 
 
 def test_rate_quality_cache():
-    ds1 = nanite.IndentationDataSet(jpkfile)
+    ds1 = nanite.IndentationGroup(jpkfile)
     idnt = ds1[0]
     idnt.apply_preprocessing(["compute_tip_position"])
 
@@ -205,7 +205,7 @@ def test_rate_quality_cache():
 
 
 def test_rate_quality_disabled():
-    ds1 = nanite.IndentationDataSet(jpkfile)
+    ds1 = nanite.IndentationGroup(jpkfile)
     idnt = ds1[0]
     idnt.apply_preprocessing(["compute_tip_position"])
 
@@ -229,7 +229,7 @@ def test_rate_quality_disabled():
 
 
 def test_rate_quality_nofit():
-    ds1 = nanite.IndentationDataSet(jpkfile)
+    ds1 = nanite.IndentationGroup(jpkfile)
     idnt = ds1[0]
     r1 = idnt.rate_quality()
     assert r1 == -1