release 0.3.0

VERSION

@@ -1 +1 @@
-0.2.1
+0.3.0

cwepr/analysis.py

@@ -33,6 +33,7 @@
 
 import aspecd.analysis
 import aspecd.dataset
+import aspecd.utils
 
 
 class FieldCalibration(aspecd.analysis.SingleAnalysisStep):
@@ -573,7 +574,7 @@ class AmplitudeVsPower(aspecd.analysis.SingleAnalysisStep):
               - PowerSweep
             result: power_sweep_analysis
           - kind: singleanalysis
-            type: PolynomialFitOnData
+            type: FitOnData
             properties:
               parameters:
                 order: 1
@@ -668,7 +669,7 @@ def _assign_units_to_result(self):
         self.result.data.axes[1].quantity = 'EPR amplitude'
 
 
-class PolynomialFitOnData(aspecd.analysis.SingleAnalysisStep):
+class FitOnData(aspecd.analysis.SingleAnalysisStep):
     """Perform polynomial fit on data and return its parameters or a dataset.
 
     Developed tests first.
@@ -689,8 +690,9 @@ class PolynomialFitOnData(aspecd.analysis.SingleAnalysisStep):
             Default: 1
 
         return_type : :class: `str`
-            Choose to returning the coefficients of the fit or a calculated
-            dataset containing the curve to plot.
+            Choose to returning the coefficients of the fit in order
+            of increasing degree or a calculated dataset containing the curve to
+            plot.
 
             Default: coefficients.
 
@@ -710,7 +712,7 @@ class PolynomialFitOnData(aspecd.analysis.SingleAnalysisStep):
     .. code-block:: yaml
 
         - kind: singleanalysis
-          type: PolynomialFitOnData
+          type: FitOnData
           properties:
             parameters:
                 points: 5
@@ -719,24 +721,22 @@ class PolynomialFitOnData(aspecd.analysis.SingleAnalysisStep):
                 add_origin: True
           result: fit
 
-<<<<<<< HEAD
-=======
     .. versionchanged:: 0.3
         Rewrite to perform fits with fixed intercept, remove parameter
         "add_origin", introduced "fixed_intercerpt".
         Return coefficients in order of increasing degree
 
->>>>>>> fd083d6... Prospector run, updated roadmap and changelog
     """
 
     def __init__(self):
         super().__init__()
-        self.description = "Perform polynomial fit and return parameters."
+        self.description = "Perform fit and return parameters."
         self.result = None
         self.parameters['points'] = 3
         self.parameters['order'] = 1
         self.parameters['return_type'] = 'coefficients'
-        self.parameters['add_origin'] = False
+        self.parameters['fixed_intercept'] = False
+        self.parameters['offset'] = 0
         self.parameters['coefficients'] = []
         # private properties
         self._curve = None
@@ -762,10 +762,12 @@ def applicable(dataset):
         return dataset.data.data.ndim == 1
 
     def _perform_task(self):
-        if self.parameters['add_origin']:
-            self._add_origin()
-        self._get_coefficients()
-        self._get_curve()
+        if self.parameters['fixed_intercept']:
+            self._linear_regression_with_fixed_intercept()
+            self._get_curve()
+        else:
+            self._get_coefficients()
+            self._get_curve()
         self._assign_result()
 
     def _get_coefficients(self):
@@ -778,21 +780,24 @@ def _get_coefficients(self):
 
     def _get_curve(self):
         self._curve = self.create_dataset()
+        slope = np.polynomial.Polynomial(self.parameters['coefficients'])
+        self._curve.data.data = slope(self.dataset.data.axes[0].values)
         self._curve.data.axes[0] = self.dataset.data.axes[0]
-        self._curve.data.data = np.polyval(self.parameters['coefficients'],
-                                           self.dataset.data.axes[0].values)
-        self._curve.data.axes[0].values = self.dataset.data.axes[0].values
 
     def _assign_result(self):
         if self.parameters['return_type'].lower() == 'dataset':
             self.result = self._curve
         else:
             self.result = self.parameters['coefficients']
 
-    def _add_origin(self):
-        self.dataset.data.axes[0].values = \
-            np.insert(self.dataset.data.axes[0].values, 0, 0)
-        self.dataset.data.data = np.insert(self.dataset.data.data, 0, 0)
+    def _linear_regression_with_fixed_intercept(self):
+        analysis = aspecd.analysis.LinearRegressionWithFixedIntercept()
+        aspecd.utils.copy_values_between_dicts(source=self.parameters,
+                                               target=analysis.parameters)
+        analysis.parameters['polynomial_coefficients'] = True
+        analysis.dataset = self.dataset
+        result = self.dataset.analyse(analysis)
+        self.parameters['coefficients'] = result.result
 
 
 class PtpVsModAmp(aspecd.analysis.SingleAnalysisStep):

cwepr/io/__init__.py

@@ -1,13 +1,25 @@
 """
 Subpackage for IO.
 
-Generally, for each file format, the importer resides in a separate module.
-The import statements below should *only* import the respective classes.
-
-Currently, in addition to modules for the individual data file formats,
-there are a series of more general modules:
-
-
+Generally, for each file format (or class of formats), the importer resides
+in a separate module.
+
+Currently, a number of more or less well-known and widely used EPR file
+formats are supported:
+
+===========================  =============  ==========================
+Format                       Extensions     Module
+===========================  =============  ==========================
+Bruker ESP and EMX           par, spc       :mod:`cwepr.io.esp_winepr`
+Bruker BES3T                 DSC, DTA       :mod:`cwepr.io.bes3t`
+Magnettech (now Bruker) XML  xml            :mod:`cwepr.io.magnettech`
+NIEHS PEST                   lmb, exp, dat  :mod:`cwepr.io.niehs`
+---------------------------  -------------  --------------------------
+Generic text file            txt            :mod:`cwepr.io.txt_file`
+===========================  =============  ==========================
+
+In addition to modules for the individual data file formats, there are a
+series of more general modules:
 
 * factory
 
@@ -20,9 +32,11 @@
 
 """
 
+# The import statements below should *only* import the respective classes.
 from .factory import DatasetImporterFactory
 from .magnettech import MagnettechXMLImporter, GoniometerSweepImporter
 from .txt_file import TxtImporter
 from .bes3t import BES3TImporter
 from .esp_winepr import ESPWinEPRImporter
+from .niehs import NIEHSDatImporter, NIEHSLmbImporter, NIEHSExpImporter
 from .exporter import ASCIIExporter, MetadataExporter

cwepr/io/factory.py

@@ -45,8 +45,11 @@ def __init__(self):
         self.supported_formats = {"BES3T": [".DTA", ".DSC"],
                                   "ESPWinEPR": [".spc", ".par"],
                                   "MagnettechXML": [".xml"],
+                                  "NIEHSDat": [".dat"],
+                                  "NIEHSLmb": [".lmb"],
+                                  "NIEHSExp": [".exp"],
                                   "Txt": [".txt"],
-                                  "Csv": [".csv"]}
+                                  }
         self.data_format = None
 
     def _get_importer(self):

cwepr/io/magnettech.py

@@ -54,7 +54,7 @@ class MagnettechXMLImporter(aspecd.io.DatasetImporter):
     """Import cw-EPR raw data from the Magnettech benchtop spectrometer.
 
     Magnettech provides a XML-file with the results. Specialities of this
-    format are existing and will be briefly explained: The data is coded in
+    format are existing and will be briefly explained: The data is encoded in
     hex numbers, and the *y* axis consists of 10 times more points than the
     *y* axis. Therefore, an interpolation is needed to expand the axis to the
     necessary amount of points.