merge upstream

Merge branch 'main' of gitea.pkm.physik.tu-darmstadt.de:IPKM/python3-damaris

.gitignore

@@ -20,6 +20,3 @@ debian/*.debhelper.log
 debian/*.debhelper
 debian/*.substvars
 debian/python3-damaris/
-
-# Agent metadata
-AGENTS.md

AGENTS.md

@@ -0,0 +1,19 @@
+# python3-damaris
+
+## GUI Purpose and Operation
+This is the front end part of GUI for controlling NMR spectrometers. On "Start", the experiment script executes and creates XML job files. A backend, not in this code, executes these jobs sequentially adn writes the results as XML files. The front end consumes these result files using the result script.
+
+## Guidelines
+1. Use the .venv python3 environment
+5. Old code was ported from gtk2 and python2.7. This code has to work on python 3.11 and above, as well as GTK3
+2. Be aware the targeted Debian versions are bookworm, trixie, and forky.
+3. Only use packages and libraries available in Debian bookworm, trixie, and forky. Make sure that the code is compatible with all of these versions.
+3. Do not commit changes (with git) or write commit messages without asking the user.
+4. Try to minimize code changes, do not use elaborate checks for defensive programming. Ask the user if something should be tested with unit tests.
+6. Use the python unittest module for unit tests, not pytest
+7. Functions for the experiment script belong to the src/damaris/experiments/Experiment.py file
+8. Functions for the result script belong in the files in the src/damaris/data/ folder
+9. The gitea workflow can be found at .gitea/workflows/debian-build.yml
+10. to not edit anything in "build", it is regenerated
+11. Use sphinx for documentation, autodoc and autosummary is used for references of all classes, functions and modules. 
+12. If a new function/method is created document a short usage the doc/api_reference.rst and a longer explanation in doc/manual.rst

doc/api_reference.rst

@@ -0,0 +1,91 @@
+#############
+API Reference
+#############
+
+This page provides an auto-generated reference of all DAMARIS classes, functions, and modules.
+It is built from docstrings using Sphinx autodoc and autosummary.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Modules:
+
+   damaris/data
+   damaris/experiments
+   damaris/gui
+   damaris/tools
+
+
+Data Module
+===========
+
+The data module contains result types, data handling, and signal processing classes.
+
+.. autosummary::
+   :toctree: _autosummary
+   :recursive:
+
+   damaris.data.ADC_Result
+   damaris.data.Accumulation
+   damaris.data.DamarisFFT
+   damaris.data.DataPool
+   damaris.data.Drawable
+   damaris.data.Errorable
+   damaris.data.Error_Result
+   damaris.data.MeasurementResult
+   damaris.data.Persistance
+   damaris.data.Resultable
+   damaris.data.Signalpath
+   damaris.data.Temperature
+   damaris.data.autophase
+
+
+Experiments Module
+==================
+
+The experiments module contains the Experiment class and related utilities for defining pulse sequences.
+
+.. autosummary::
+   :toctree: _autosummary
+   :recursive:
+
+   damaris.experiments.Experiment
+   damaris.experiments.DurationEstimator
+   damaris.experiments.dac
+
+
+GUI Module
+==========
+
+The GUI module contains the graphical interface, backend driver, and experiment/result handling.
+
+.. autosummary::
+   :toctree: _autosummary
+   :recursive:
+
+   damaris.gui.BackendDriver
+   damaris.gui.DamarisGUI
+   damaris.gui.ExperimentHandling
+   damaris.gui.ExperimentWriter
+   damaris.gui.ResultHandling
+   damaris.gui.ResultReader
+   damaris.gui.TemperatureMonitor
+   damaris.gui.logging_utils
+
+
+Tools Module
+============
+
+The tools module contains hardware driver interfaces and utility functions.
+
+.. autosummary::
+   :toctree: _autosummary
+   :recursive:
+
+   damaris.tools.eurotherm
+   damaris.tools.flow_control
+   damaris.tools.goniometer
+   damaris.tools.lakeshore
+   damaris.tools.ranges
+   damaris.tools.signal
+   damaris.tools.temperature
+   damaris.tools.temperature_simulator

doc/conf.py

@@ -21,9 +21,13 @@ release = damaris.__version__
 
 extensions = [
     'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
     'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
     'sphinxcontrib.bibtex',
     ]
+
+autosummary_generate = True
 bibtex_bibfiles = ['bibdesk_db.bib']
 bibtex_bibstyles = ['numeric']
 bibtex_citestyle = 'numeric'

src/damaris/data/ADC_Result.py

@@ -98,6 +98,7 @@ class ADC_Result(Resultable, Drawable, DamarisFFT, Signalpath):
             self.y.append(numpy.zeros((samples,), dtype="int16"))
 
         self.x = numpy.zeros((samples,), dtype="float32")
+        self.nChannels = channels
 
         self.index.append((0, samples-1))
         self.cont_data = True
@@ -231,6 +232,8 @@ class ADC_Result(Resultable, Drawable, DamarisFFT, Signalpath):
                 job_id=self.job_id,
                 job_date=self.job_date,
             )
+            r.nChannels = self.nChannels
+            r.is_clipped = self.is_clipped
         finally:
             self.lock.release()
 
@@ -274,6 +277,8 @@ class ADC_Result(Resultable, Drawable, DamarisFFT, Signalpath):
             tmp_y.append(self.y[i][start:end+1].copy())
 
         r = ADC_Result(x = tmp_x, y = tmp_y,  index = [(0,len(tmp_y[0])-1)], sampl_freq = self.sampling_rate, desc = self.description.copy() if self.description is not None else None, job_id = self.job_id, job_date = self.job_date)
+        r.nChannels = self.nChannels
+        r.is_clipped = self.is_clipped
         self.lock.release()
         return r
 

src/damaris/data/Accumulation.py

@@ -111,21 +111,22 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath):
             self.lock.release()
             raise
 
-        tmp_x = self.x[start:end+1]
+        tmp_x = self.x[start:end+1].copy()
         tmp_y = []
 
         for i in range(self.get_number_of_channels()):
-            tmp_y.append(self.y[i][start:end+1])
+            tmp_y.append(self.y[i][start:end+1].copy())
 
-        r = Accumulation(x = tmp_x, y = tmp_y, n = self.n, index = [(0,len(tmp_y[0])-1)], sampl_freq = self.sampling_rate, error = self.use_error)            
+        r = Accumulation(x = tmp_x, y = tmp_y, n = self.n, index = [(0,len(tmp_y[0])-1)], sampl_freq = self.sampling_rate, error = self.use_error)
         if self.uses_statistics():
             r.y_square = []
             for i in range(self.get_number_of_channels()):
-                r.y_square.append(self.y_square[i][start:end+1])
+                r.y_square.append(self.y_square[i][start:end+1].copy())
         if self.common_descriptions is not None:
             r.common_descriptions = self.common_descriptions.copy()
         r.time_period = self.time_period[:]
         r.job_ids = self.job_ids.copy()
+        r.is_clipped = self.is_clipped
         self.lock.release()
         return r
 

src/damaris/gui/ResultReader.py

@@ -231,7 +231,6 @@ class ResultReader:
                 for i in range(nChannels):
                     # split interleaved data
                     self.result.y[i][tmp_index:tmp_index+tmp_size] = tmp_part[i::nChannels]
-                    self.result.y[i][tmp_index:tmp_index+tmp_size] = tmp_part[i::nChannels]
 
                 if self.result.index != []:
                     self.result.index.append((tmp_index, tmp_index+tmp_size-1))

tests/test_ADC_Result.py

@@ -64,6 +64,7 @@ class TestADCResult(unittest.TestCase):
         self.assertTrue(np.array_equal(adc.x, np.zeros(3, dtype="float32")))
         self.assertTrue(np.array_equal(adc.y[0], np.zeros(3, dtype="int16")))
         self.assertEqual(adc.index, [(0, 2)])
+        self.assertEqual(adc.nChannels, 2)
 
     def test_add_sample_space(self):
         """Test adding sample space."""
@@ -90,6 +91,33 @@ class TestADCResult(unittest.TestCase):
         self.assertEqual(sub_result.description, {"key": "value"})
         self.assertEqual(sub_result.job_id, 42)
 
+    def test_get_result_by_index_copies_nChannels_and_is_clipped(self):
+        """Test that get_result_by_index properly copies nChannels and is_clipped."""
+        adc = self.create_adc_result()
+        adc.index = [(0, 1), (1, 2)]
+        adc.set_nChannels(2)
+        adc.is_clipped = True
+
+        sub_result = adc.get_result_by_index(1)
+
+        self.assertEqual(sub_result.nChannels, 2)
+        self.assertEqual(sub_result.is_clipped, True)
+
+    def test_get_result_by_index_data_independence(self):
+        """Test that get_result_by_index returns independent data (not shared views)."""
+        adc = self.create_adc_result()
+        adc.index = [(0, 1), (1, 2)]
+        original_x = adc.x.copy()
+        original_data = adc.y[0].copy()
+
+        sub_result = adc.get_result_by_index(1)
+        sub_result.y[0][0] = 9999
+        sub_result.x[0] = 999.0
+
+        self.assertEqual(sub_result.y[0][0], 9999)
+        self.assertTrue(np.array_equal(adc.y[0], original_data))
+        self.assertTrue(np.array_equal(adc.x, original_x))
+
     def test_set_sampling_rate(self):
         """Test updating the sampling rate."""
         adc = ADC_Result()

tests/test_Accumulation.py

@@ -107,6 +107,35 @@ class TestAccumulation(unittest.TestCase):
         self.assertEqual(sub_result.index, [(0, 1)])
         self.assertEqual(sub_result.common_descriptions, {"key": "value"})
 
+    def test_get_accu_by_index_copies_is_clipped(self):
+        """Test that get_accu_by_index properly copies is_clipped."""
+        adc = self.create_adc_result()
+        adc.index = [(0, 1), (1, 2)]
+        accu = Accumulation()
+        accu += adc
+        accu.is_clipped = True
+
+        sub_result = accu.get_accu_by_index(1)
+
+        self.assertEqual(sub_result.is_clipped, True)
+
+    def test_get_accu_by_index_data_independence(self):
+        """Test that get_accu_by_index returns independent data (not shared views)."""
+        adc = self.create_adc_result()
+        adc.index = [(0, 1), (1, 2)]
+        accu = Accumulation()
+        accu += adc
+        original_y0 = accu.y[0].copy()
+
+        sub_result = accu.get_accu_by_index(1)
+        sub_result.y[0][0] = 9999
+        sub_result.x[0] = 999.0
+
+        self.assertEqual(sub_result.y[0][0], 9999)
+        self.assertTrue(np.array_equal(accu.y[0], original_y0))
+        # x array should also be independent
+        self.assertEqual(accu.x[1], 1.0)
+
     def test_write_to_csv_without_error(self):
         """Test the functionality of writing to CSV."""
         from io import StringIO