Adding thumbnail generating function

.gitignore

@@ -27,4 +27,6 @@ nrnivmodl.log
 *.btr
 *.whl
 .ipynb_checkpoints
-cADpyr_L2TPC_dendrogram.png
+cADpyr_L2TPC_dendrogram.png
+temp/
+venv/

bluecellulab/analysis/plotting.py

@@ -2,6 +2,140 @@
 
 import matplotlib.pyplot as plt
 import pathlib
+import numpy as np
+from typing import Optional, Tuple
+from bluecellulab.tools import calculate_rheobase
+from bluecellulab.circuit.circuit_access import EmodelProperties
+from bluecellulab.cell import Cell
+from bluecellulab.simulation.neuron_globals import NeuronGlobals
+from bluecellulab import Simulation
+
+
+def generate_cell_thumbnail(
+    template_path: str,
+    morphology_path: Optional[str] = None,
+    threshold_current: Optional[float] = None,
+    holding_current: Optional[float] = None,
+    template_format: str = "v6",
+    save_figure: bool = True,
+    output_path: str = "cell_thumbnail.png",
+    show_figure: bool = False,
+    v_init: Optional[float] = -80.0,
+    celsius: Optional[float] = 34.0,
+) -> Tuple[np.ndarray, np.ndarray]: 
+    """Generate a thumbnail image of a Cell object's step response.
+
+    Args:
+        template_path: Path to the hoc file.
+        morphology_path: Path to the morphology file. Default is None.
+        threshold_current: Threshold current for the cell. Default is None.
+        holding_current: Holding current for the cell. Default is None.
+        template_format: Template format. Default is "v6".
+        save_figure: Whether to save the figure. Default is True.
+        output_path: Path where to save the thumbnail image.
+        show_figure: Whether to display the figure. Default is False.
+        v_init: Initial membrane potential. Default is -80.0 mV.
+        celsius: Temperature in Celsius. Default is 34.0.
+
+    Returns:
+        Tuple containing (time, voltage) arrays of the simulation.
+    """
+    # If the threshold and holding_current is not known,
+    # we use calculate_rheobase() to find the threshold_current.
+    # For this case, we set the holding_current to 0.0 nA.
+    # if threshold_current is None: 
+    threshold_current = 1.0
+    if holding_current is None:
+        holding_current = 0.0
+
+    emodel_properties = EmodelProperties(
+        threshold_current=threshold_current,
+        holding_current=holding_current
+    )
+
+    # Initialise cell
+    thumbnail_cell = Cell(
+        template_path=template_path,
+        morphology_path=morphology_path,
+        template_format=template_format,
+        emodel_properties=emodel_properties,
+    )
+    holding_current = 0.0
+    # Calculate rheobase
+    newthreshold_current = calculate_rheobase(
+        thumbnail_cell,
+        section="soma[0]",
+        segx=0.5
+    )
+    print(f"Threshold current: {newthreshold_current}")
+    print(f"Holding current: {holding_current}")
+    #delete thumbnail_cell
+    thumbnail_cell.delete()
+
+    # Update emodel properties
+    emodel_properties = EmodelProperties(
+        threshold_current=newthreshold_current,
+        holding_current=holding_current
+    )
+
+    # Create cell
+    thumbnail_cell = Cell(
+        template_path=template_path,
+        morphology_path=morphology_path,
+        template_format=template_format,
+        emodel_properties=emodel_properties,
+    )
+
+    # Add 130% threshold current injection
+    step_amplitude = newthreshold_current * 1.1
+    step_duration = 2000
+    start_time = 700
+    thumbnail_cell.add_step(
+        start_time=start_time,
+        stop_time=start_time+step_duration,
+        level=step_amplitude
+    )
+
+    # Set up simulation
+    sim = thumbnail_cell.simulation if hasattr(thumbnail_cell, 'simulation') else None
+    if sim is None:
+        sim = Simulation()
+        sim.add_cell(thumbnail_cell)
+
+    neuron_globals = NeuronGlobals.get_instance()
+    # neuron_globals.temperature = celsius
+    # neuron_globals.v_init = v_init
+
+    # Run simulation
+    tstop = step_duration+300
+    sim.run(tstop)
+    # Get recording data
+    time = thumbnail_cell.get_time()
+    voltage = thumbnail_cell.get_soma_voltage()
+
+    # Create figure with default size (matplotlib's default is [6.4, 4.8])
+    fig, ax = plt.subplots(figsize=(6.4, 4.8))
+    ax.plot(time, voltage, 'k-', linewidth=1.5)
+    ax.set_xlabel('Time (ms)', fontsize=10)
+    ax.set_ylabel('Membrane potential (mV)', fontsize=10)
+    plt.tight_layout()
+
+    if save_figure:
+        # Create parent directories if they don't exist
+        output_path = pathlib.Path(output_path)
+        output_path.parent.mkdir(parents=True, exist_ok=True)
+
+        # Save figure with 300 DPI
+        plt.savefig(output_path, dpi=300, bbox_inches='tight')
+
+    if show_figure:
+        plt.show()
+    else:
+        plt.close()
+
+    thumbnail_cell.delete()
+
+    return time, voltage
 
 
 def plot_iv_curve(

tests/test_analysis_plotting.py

@@ -0,0 +1,140 @@
+"""Tests for analysis plotting functions."""
+import tempfile
+from pathlib import Path
+from typing import Optional, Tuple
+import pytest
+import numpy as np
+from bluecellulab.analysis.plotting import generate_cell_thumbnail
+from bluecellulab.circuit.circuit_access.definition import EmodelProperties
+
+# Test data paths
+TEST_DATA_DIR = (Path(__file__).parent / "examples" 
+                 / "circuit_sonata_quick_scx" / "components")
+HOC_FILE = TEST_DATA_DIR / "hoc" / "cADpyr_L2TPC.hoc"
+MORPH_FILE = TEST_DATA_DIR / "morphologies" / "asc" / "rr110330_C3_idA.asc"
+
+# Fixtures
+@pytest.fixture(scope="module")
+def emodel_properties() -> EmodelProperties:
+    """Fixture providing default emodel properties for testing."""
+    return EmodelProperties(threshold_current=1.1433533430099487,
+                            holding_current=1.4146618843078613,
+                            AIS_scaler=1.4561502933502197,
+                            soma_scaler=1.0)
+
+@pytest.fixture
+def output_dir():
+    """Fixture providing a temporary directory for test outputs."""
+    with tempfile.TemporaryDirectory() as temp_dir:
+        yield Path(temp_dir)
+
+class TestGenerateCellThumbnail:
+    """Test cases for generate_cell_thumbnail function."""
+
+    def test_with_explicit_output_path(self, output_dir: Path, emodel_properties: EmodelProperties):
+        """Test thumbnail generation with explicit output path."""
+        # Skip test if required files don't exist
+        if not HOC_FILE.exists() or not MORPH_FILE.exists():
+            pytest.skip("Required test files not found")
+
+        # Arrange
+        output_path = output_dir / "cell_thumbnail.png"
+
+        # Act
+        time, voltage = generate_cell_thumbnail(
+            template_path=str(HOC_FILE),
+            morphology_path=str(MORPH_FILE),
+            template_format="v6",
+            emodel_properties=emodel_properties,
+            output_path=output_path
+        )
+
+        # Assert
+        assert output_path.exists(), "Thumbnail file was not created"
+        assert output_path.stat().st_size > 0, "Thumbnail file is empty"
+        assert len(time) == len(voltage) > 0, "Time and voltage arrays should have matching lengths"
+        assert isinstance(time, np.ndarray), "Time should be a numpy array"
+        assert isinstance(voltage, np.ndarray), "Voltage should be a numpy array"
+
+    def test_with_default_output_path(self, tmp_path, emodel_properties: EmodelProperties):
+        """Test thumbnail generation with default output path."""
+        # Skip test if required files don't exist
+        if not HOC_FILE.exists() or not MORPH_FILE.exists():
+            pytest.skip("Required test files not found")
+
+        # Arrange
+        default_path = Path("cell_thumbnail.png")
+
+        try:
+            # Act
+            time, voltage = generate_cell_thumbnail(
+                template_path=str(HOC_FILE),
+                morphology_path=str(MORPH_FILE),
+                template_format="v6",
+                emodel_properties=emodel_properties
+            )
+
+            # Assert
+            assert default_path.exists(), "Default thumbnail file was not created"
+            assert default_path.stat().st_size > 0, "Default thumbnail file is empty"
+            assert len(time) > 0 and len(voltage) > 0, "Output arrays should not be empty"
+        finally:
+            # Cleanup
+            if default_path.exists():
+                default_path.unlink()
+
+    @pytest.mark.parametrize("threshold_value", [0, None])
+    def test_without_threshold(self, output_dir: Path, emodel_properties: EmodelProperties, threshold_value: Optional[float]):
+        """Test thumbnail generation when threshold needs to be calculated."""
+        # Skip test if required files don't exist
+        if not HOC_FILE.exists() or not MORPH_FILE.exists():
+            pytest.skip("Required test files not found")
+
+        # Arrange
+        output_path = output_dir / "cell_no_threshold.png"
+
+        # Create a copy of emodel_properties with no threshold
+        test_props = EmodelProperties(
+            threshold_current=0.0 if threshold_value == 0 else 0.1,  # Will trigger calculate_rheobase
+            holding_current=emodel_properties.holding_current,
+            AIS_scaler=emodel_properties.AIS_scaler,
+            soma_scaler=emodel_properties.soma_scaler
+        )
+
+        # Act
+        time, voltage = generate_cell_thumbnail(
+            template_path=str(HOC_FILE),
+            morphology_path=str(MORPH_FILE),
+            template_format="v6",
+            emodel_properties=test_props,
+            output_path=output_path
+        )
+
+        # Assert
+        assert output_path.exists(), "Thumbnail file was not created"
+        assert output_path.stat().st_size > 0, "Thumbnail file is empty"
+        assert len(time) > 0 and len(voltage) > 0, "Output arrays should not be empty"
+
+    @pytest.mark.parametrize("show_figure", [True, False])
+    def test_show_figure_parameter(self, output_dir: Path, emodel_properties: EmodelProperties, show_figure: bool):
+        """Test that show_figure parameter works as expected."""
+        # Skip test if required files don't exist
+        if not HOC_FILE.exists() or not MORPH_FILE.exists():
+            pytest.skip("Required test files not found")
+
+        # Arrange
+        output_path = output_dir / f"show_figure_{show_figure}.png"
+
+        # Act
+        time, voltage = generate_cell_thumbnail(
+            template_path=str(HOC_FILE),
+            morphology_path=str(MORPH_FILE),
+            template_format="v6",
+            emodel_properties=emodel_properties,
+            output_path=output_path,
+            show_figure=show_figure
+        )
+
+        # Assert
+        assert output_path.exists(), "Thumbnail file was not created"
+        assert output_path.stat().st_size > 0, "Thumbnail file is empty"