FlowCyPy 0.5.7__tar.gz → 0.5.8__tar.gz

{flowcypy-0.5.7 → flowcypy-0.5.8}/FlowCyPy/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.5.7'
-__version_tuple__ = version_tuple = (0, 5, 7)
+__version__ = version = '0.5.8'
+__version_tuple__ = version_tuple = (0, 5, 8)

{flowcypy-0.5.7 → flowcypy-0.5.8}/FlowCyPy/cytometer.py

@@ -76,6 +76,7 @@ class FlowCytometer:
         self.detectors = detectors
         self.coupling_mechanism = coupling_mechanism
         self.background_power = background_power
+        self.plot = self.PlotInterface(self)
 
         assert len(self.detectors) == 2, 'For now, FlowCytometer can only take two detectors for the analysis.'
         assert self.detectors[0].name != self.detectors[1].name, 'Both detectors cannot have the same name'
@@ -85,7 +86,7 @@ class FlowCytometer:
         Computes and assigns the optical coupling power for each particle-detection event.
 
         This method evaluates the coupling between the scatterers in the flow cell and the detectors
-        using the specified detection mechanism. The computed coupling power is stored in the 
+        using the specified detection mechanism. The computed coupling power is stored in the
         `scatterer_collection` dataframe under detector-specific columns.
 
         Updates
@@ -98,7 +99,7 @@ class FlowCytometer:
         ------
         ValueError
             If an invalid coupling mechanism is specified during initialization.
-        """        
+        """
         detection_mechanism = self._get_detection_mechanism()
 
         for detector in self.detectors:
@@ -109,7 +110,7 @@ class FlowCytometer:
             )
 
             self.scatterer_collection.dataframe["detector: " + detector.name] = pint_pandas.PintArray(self.coupling_power, dtype=self.coupling_power.units)
-        
+
         self._generate_pulse_parameters()
 
     def initialize_signal(self) -> None:
@@ -124,11 +125,11 @@ class FlowCytometer:
         Each detector's `raw_signal` attribute is initialized with time-dependent values
         based on the flow cell's runtime.
 
-        """        
+        """
         # Initialize the detectors
         for detector in self.detectors:
             detector.source = self.source
-            detector.init_raw_signal(run_time=self.flow_cell.run_time)     
+            detector.init_raw_signal(run_time=self.flow_cell.run_time)
 
     def simulate_pulse(self) -> None:
         """
@@ -260,84 +261,13 @@ class FlowCytometer:
         )
 
         self.pulse_dataframe = pd.DataFrame(columns=columns)
-                
+
         self.pulse_dataframe['Centers'] = self.scatterer_collection.dataframe['Time']
 
         widths = self.source.waist / self.flow_cell.flow_speed * np.ones(self.scatterer_collection.n_events)
 
         self.scatterer_collection.dataframe['Widths'] = pint_pandas.PintArray(widths, dtype=widths.units)
 
-    def plot(self, figure_size: tuple = (10, 6), add_peak_locator: bool = False, show: bool = True) -> None:
-        """
-        Visualizes the raw signals for all detector channels along with the scatterer distribution.
-
-        Parameters
-        ----------
-        figure_size : tuple, optional
-            Dimensions of the generated plot (default: (10, 6)).
-        add_peak_locator : bool, optional
-            If True, adds visual markers for detected signal peaks (default: False).
-
-        Effects
-        -------
-        Displays a multi-panel plot showing:
-        - Raw signals for each detector channel.
-        - Scatterer distribution along the time axis.
-        """
-        logging.info("Plotting the signal for the different channels.")
-
-        n_detectors = len(self.detectors)
-
-        with plt.style.context(mps):
-            _, axes = plt.subplots(ncols=1, nrows=n_detectors + 1, figsize=figure_size, sharex=True, sharey=True, gridspec_kw={'height_ratios': [1, 1, 0.4]})
-
-        time_unit, signal_unit = self.detectors[0].plot(ax=axes[0], show=False, add_peak_locator=add_peak_locator)
-        self.detectors[1].plot(ax=axes[1], show=False, time_unit=time_unit, signal_unit=signal_unit, add_peak_locator=add_peak_locator)
-
-        axes[-1].get_yaxis().set_visible(False)
-        self.scatterer_collection.add_to_ax(axes[-1])
-
-        # Add legends to each subplot
-        for ax in axes:
-            ax.legend()
-
-        if show: # Display the plot
-            plt.show()       
-
-    def plot_coupling_density(self, log_scale: bool = False, show: bool = True) -> None:
-        """
-        Plots the density distribution of optical coupling in the FSC and SSC channels.
-
-        This method generates a joint plot showing the relationship between the signals from
-        the forward scatter ('detector: forward') and side scatter ('detector: side') detectors.
-        The plot is color-coded by particle population and can optionally display axes on a logarithmic scale.
-
-        Parameters
-        ----------
-        log_scale : bool, optional
-            If True, applies a logarithmic scale to both the x and y axes of the plot (default: False).
-        show : bool, optional
-            If True, displays the plot immediately. If False, the plot is created but not displayed,
-            allowing for further customization or saving externally (default: True).
-
-        """
-        with plt.style.context(mps):
-            joint_plot = sns.jointplot(
-                data=self.scatterer_collection.dataframe,
-                y='detector: side',
-                x='detector: forward',
-                hue="Population",
-                alpha=0.8,
-            )
-
-
-        if log_scale:
-            joint_plot.ax_joint.set_xscale('log')
-            joint_plot.ax_joint.set_yscale('log')    
-
-        if show: # Display the plot
-            plt.show()            
-
     def add_detector(self, **kwargs) -> Detector:
         """
         Dynamically adds a new detector to the system configuration.
@@ -355,9 +285,112 @@ class FlowCytometer:
         Effects
         -------
         - Appends the created detector to the `detectors` list.
-        """        
+        """
         detector = Detector(**kwargs)
 
         self.detectors.append(detector)
 
         return detector
+
+    class PlotInterface:
+        def __init__(self, cytometer):
+            self.cytometer = cytometer
+
+        def signals(self, figure_size: tuple = (10, 6), add_peak_locator: bool = False, show: bool = True) -> None:
+            """
+            Visualizes the raw signals for all detector channels along with the scatterer distribution.
+
+            Parameters
+            ----------
+            figure_size : tuple, optional
+                Dimensions of the generated plot (default: (10, 6)).
+            add_peak_locator : bool, optional
+                If True, adds visual markers for detected signal peaks (default: False).
+
+            Effects
+            -------
+            Displays a multi-panel plot showing:
+            - Raw signals for each detector channel.
+            - Scatterer distribution along the time axis.
+            """
+            logging.info("Plotting the signal for the different channels.")
+
+            scatterer_collection = self.cytometer.scatterer_collection
+            detectors = self.cytometer.detectors
+
+            n_detectors = len(detectors)
+
+            with plt.style.context(mps):
+                _, axes = plt.subplots(ncols=1, nrows=n_detectors + 1, figsize=figure_size, sharex=True, sharey=True, gridspec_kw={'height_ratios': [1, 1, 0.4]})
+
+            time_unit, signal_unit = detectors[0].plot(ax=axes[0], show=False, add_peak_locator=add_peak_locator)
+            detectors[1].plot(ax=axes[1], show=False, time_unit=time_unit, signal_unit=signal_unit, add_peak_locator=add_peak_locator)
+
+            axes[-1].get_yaxis().set_visible(False)
+            scatterer_collection.add_to_ax(axes[-1])
+
+            # Add legends to each subplot
+            for ax in axes:
+                ax.legend()
+
+            if show: # Display the plot
+                plt.show()
+
+        def coupling_distribution(self, log_scale: bool = False, show: bool = True, equal_limits: bool = False, save_path: str = None) -> None:
+            """
+            Plots the density distribution of optical coupling in the FSC and SSC channels.
+
+            This method generates a joint plot showing the relationship between the signals from
+            the forward scatter ('detector: forward') and side scatter ('detector: side') detectors.
+            The plot is color-coded by particle population and can optionally display axes on a logarithmic scale.
+
+            Parameters
+            ----------
+            log_scale : bool, optional
+                If True, applies a logarithmic scale to both the x and y axes of the plot (default: False).
+            show : bool, optional
+                If True, displays the plot immediately. If False, the plot is created but not displayed,
+                allowing for further customization or saving externally (default: True).
+            equal_limits : bool, optional
+                If True, sets the same limits for both the x and y axes based on the maximum range
+                across both axes. If False, the limits are set automatically based on the data (default: False).
+
+            """
+            scatterer_collection = self.cytometer.scatterer_collection
+            detector_0, detector_1 = self.cytometer.detectors
+
+            with plt.style.context(mps):
+                joint_plot = sns.jointplot(
+                    data=scatterer_collection.dataframe,
+                    x=f'detector: {detector_0.name}',
+                    y=f'detector: {detector_1.name}',
+                    hue="Population",
+                    alpha=0.8,
+                )
+
+            if log_scale:
+                joint_plot.ax_joint.set_xscale('log')
+                joint_plot.ax_joint.set_yscale('log')
+
+            if equal_limits:
+                # Get data limits
+                x_data = scatterer_collection.dataframe[f'detector: {detector_0.name}']
+                y_data = scatterer_collection.dataframe[f'detector: {detector_1.name}']
+
+                x_min, x_max = x_data.min(), x_data.max()
+                y_min, y_max = y_data.min(), y_data.max()
+
+                # Find the overall min and max
+                overall_min = min(x_min, y_min)
+                overall_max = max(x_max, y_max)
+
+                # Set equal limits
+                joint_plot.ax_joint.set_xlim(overall_min, overall_max)
+                joint_plot.ax_joint.set_ylim(overall_min, overall_max)
+
+            if save_path:
+                joint_plot.figure.savefig(save_path, dpi=300, bbox_inches='tight')
+                print(f"Plot saved to {save_path}")
+
+            if show:  # Display the plot
+                plt.show()

{flowcypy-0.5.7 → flowcypy-0.5.8}/FlowCyPy/flow_cell.py

@@ -130,14 +130,14 @@ class FlowCell(object):
             ['Flow Area', f"{self.flow_area:.2f~#P}"],
             ['Total Time', f"{self.run_time:.2f~#P}"]
         ]
-    
+
     # def initialize(self, scatterer: Population | ScattererCollection) -> None:
     #     if isinstance(scatterer, Population):
     #         return self._initialize_population(scatterer)
 
     #     elif isinstance(scatterer, ScattererCollection):
     #         return self._initialize_scatterer_collection(scatterer)
-    
+
     def _initialize_population(self, population: Population) -> None:
         population.dataframe = pandas.DataFrame()
 
@@ -164,13 +164,13 @@ class FlowCell(object):
         scatterer : Scatterer
             An instance of the Scatterer class that describes the scatterer collection being used.
 
-        """        
+        """
         self.scatterer_collection = scatterer_collection
 
         for population in self.scatterer_collection.populations:
             self._initialize_population(population)
             population.dataframe.Size = population.dataframe.Size.pint.to(size_units)
-        
+
         if len(self.scatterer_collection.populations) != 0:
             self.scatterer_collection.dataframe = pandas.concat(
                 [population.dataframe for population in self.scatterer_collection.populations],
@@ -195,7 +195,7 @@ class FlowCell(object):
                 index=multi_index
             )
 
-        self.scatterer_collection.n_events = len(self.scatterer_collection.dataframe)        
+        self.scatterer_collection.n_events = len(self.scatterer_collection.dataframe)
 
     def distribute_time_linearly(self, sequential_population: bool = False) -> None:
         """
@@ -210,14 +210,14 @@ class FlowCell(object):
 
         """
         # Generate linearly spaced time values across the flow cell runtime
-        linear_spacing = numpy.linspace(0, self.run_time, self.n_events)
+        linear_spacing = numpy.linspace(0, self.run_time, self.scatterer_collection.n_events)
 
         # Optionally randomize the linear spacing
         if not sequential_population:
             numpy.random.shuffle(linear_spacing)
 
         # Assign the linearly spaced or randomized times to the scatterer DataFrame
-        self.scatterer_collectionscatterer.dataframe.Time = PintArray(linear_spacing, dtype=self.scatterer_collection.dataframe.Time.pint.units)        
+        self.scatterer_collection.dataframe.Time = PintArray(linear_spacing, dtype=self.scatterer_collection.dataframe.Time.pint.units)
 
     def _generate_longitudinal_positions(self, population: Population) -> None:
         r"""

{flowcypy-0.5.7 → flowcypy-0.5.8}/FlowCyPy/noises.py

@@ -1,6 +1,11 @@
+class RestrictiveMeta(type):
+    def __setattr__(cls, name, value):
+        if not hasattr(cls, name):
+            raise AttributeError(f"Cannot set unknown class-level attribute '{name}' in {cls.__name__}.")
+        super().__setattr__(name, value)
 
 
-class NoiseSetting:
+class NoiseSetting(metaclass=RestrictiveMeta):
     _instance = None
 
     def __new__(cls, *args, **kwargs):

{flowcypy-0.5.7 → flowcypy-0.5.8}/FlowCyPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: FlowCyPy
-Version: 0.5.7
+Version: 0.5.8
 Summary: A package for flow-cytometry simulations.
 Author-email: Martin Poinsinet de Sivry-Houle <martin.poinsinet.de.sivry@gmail.com>
 License: MIT License

{flowcypy-0.5.7 → flowcypy-0.5.8}/FlowCyPy.egg-info/SOURCES.txt

@@ -54,6 +54,7 @@ FlowCyPy/peak_locator/basic.py
 FlowCyPy/peak_locator/derivative.py
 FlowCyPy/peak_locator/moving_average.py
 developments/doc/internship.pdf
+developments/scripts/concentration_comparison.py
 developments/scripts/create_images.py
 developments/scripts/data_analysis.py
 developments/scripts/dev_beads_analysis.py
@@ -82,6 +83,7 @@ docs/examples/noise_sources/dark_current.py
 docs/examples/noise_sources/shot_noise.py
 docs/examples/noise_sources/thermal.py
 docs/examples/tutorials/README.rst
+docs/examples/tutorials/limit_of_detection.py
 docs/examples/tutorials/workflow.py
 docs/images/example_0.png
 docs/images/example_1.png

{flowcypy-0.5.7 → flowcypy-0.5.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: FlowCyPy
-Version: 0.5.7
+Version: 0.5.8
 Summary: A package for flow-cytometry simulations.
 Author-email: Martin Poinsinet de Sivry-Houle <martin.poinsinet.de.sivry@gmail.com>
 License: MIT License

flowcypy-0.5.8/developments/scripts/concentration_comparison.py

@@ -0,0 +1,109 @@
+
+import numpy as np
+from FlowCyPy import FlowCytometer, ScattererCollection, EventCorrelator, Detector, GaussianBeam, FlowCell
+from FlowCyPy import peak_locator
+from FlowCyPy.units import particle, milliliter, nanometer, RIU, second, micrometer, millisecond, meter
+from FlowCyPy.units import degree, watt, ampere, millivolt, ohm, kelvin, milliampere, megahertz, microvolt
+from FlowCyPy.units import microsecond
+from FlowCyPy.units import milliwatt, AU
+from FlowCyPy import NoiseSetting
+from FlowCyPy import Population, distribution
+from FlowCyPy.population import Exosome, HDL
+
+NoiseSetting.include_noises = True
+
+np.random.seed(3)
+
+source = GaussianBeam(
+    numerical_aperture=0.3 * AU,             # Numerical aperture of the laser: 0.3
+    wavelength=488 * nanometer,              # Laser wavelength: 800 nanometers
+    optical_power=100 * milliwatt             # Laser optical power: 10 milliwatts
+)
+
+flow_cell = FlowCell(
+    source=source,
+    flow_speed=7.56 * meter / second,      # Flow speed: 7.56 meters per second
+    flow_area=(10 * micrometer) ** 2,      # Flow area: 10 x 10 micrometers
+    run_time=.2 * millisecond             # Total simulation time: 0.3 milliseconds
+)
+
+scatterer = ScattererCollection(medium_refractive_index=1.33 * RIU)  # Medium refractive index: 1.33
+
+population_0 = Population(
+    name='Pop 0',
+    particle_count=100 * particle,
+    size=distribution.RosinRammler(characteristic_size=100 * nanometer, spread=4.5),
+    refractive_index=distribution.Normal(mean=1.39 * RIU, std_dev=0.02 * RIU)
+)
+
+scatterer.add_population(population_0)
+# scatterer.add_population(hdl)
+
+
+flow_cell.initialize(scatterer_collection=scatterer)
+
+scatterer._log_properties()
+
+source.print_properties()  # Print the laser source properties
+
+detector_0 = Detector(
+    name='side',                             # Detector name: Side scatter detector
+    phi_angle=90 * degree,                   # Angle: 90 degrees (Side Scatter)
+    numerical_aperture=.2 * AU,             # Numerical aperture: 1.2
+    responsitivity=1 * ampere / watt,        # Responsitivity: 1 ampere per watt
+    sampling_freq=60 * megahertz,            # Sampling frequency: 60 MHz
+    saturation_level=0.04 * millivolt,          # Saturation level: 2 millivolts
+    # n_bins='16bit',                          # Number of bins: 14-bit resolution
+    resistance=50 * ohm,                     # Detector resistance: 50 ohms
+    dark_current=0.1 * milliampere,          # Dark current: 0.1 milliamps
+    temperature=300 * kelvin                 # Operating temperature: 300 Kelvin
+)
+
+detector_1 = Detector(
+    name='forward',                          # Detector name: Forward scatter detector
+    phi_angle=0 * degree,                    # Angle: 0 degrees (Forward Scatter)
+    numerical_aperture=.2 * AU,             # Numerical aperture: 1.2
+    responsitivity=1 * ampere / watt,        # Responsitivity: 1 ampere per watt
+    sampling_freq=60 * megahertz,            # Sampling frequency: 60 MHz
+    saturation_level=0.04 * millivolt,          # Saturation level: 2 millivolts
+    # n_bins='16bit',                          # Number of bins: 14-bit resolution
+    resistance=50 * ohm,                     # Detector resistance: 50 ohms
+    dark_current=0.1 * milliampere,          # Dark current: 0.1 milliamps
+    temperature=300 * kelvin                 # Operating temperature: 300 Kelvin
+)
+
+
+detector_1.print_properties()  # Print the properties of the forward scatter detector
+
+cytometer = FlowCytometer(                      # Laser source used in the experiment
+    flow_cell=flow_cell,                     # Populations used in the experiment
+    background_power=0.0 * milliwatt,
+    detectors=[detector_0, detector_1]       # List of detectors: Side scatter and Forward scatter
+)
+
+cytometer.run_coupling_analysis()
+
+cytometer.initialize_signal()
+
+cytometer.simulate_pulse()
+
+cytometer.plot.signals()
+
+algorithm = peak_locator.MovingAverage(
+    threshold=10 * microvolt,       # Signal threshold: 0.1 mV
+    window_size=1 * microsecond,         # Moving average window size: 1 µs
+    min_peak_distance=0.1 * microsecond  # Minimum distance between peaks: 0.3 µs
+)
+
+detector_0.set_peak_locator(algorithm)
+detector_1.set_peak_locator(algorithm)
+
+cytometer.plot.signals(add_peak_locator=True)
+
+analyzer = EventCorrelator(cytometer=cytometer)
+
+analyzer.run_analysis(compute_peak_area=False)
+
+analyzer.get_coincidence(margin=0.1 * microsecond)
+
+analyzer.plot(log_plot=False)

flowcypy-0.5.8/developments/scripts/dev_temp.py

@@ -0,0 +1,96 @@
+import numpy as np
+from FlowCyPy import FlowCell
+from FlowCyPy.units import meter, micrometer, millisecond, second, degree
+from FlowCyPy import ScattererCollection
+from FlowCyPy.units import particle, milliliter, nanometer, RIU, milliwatt, AU
+from FlowCyPy import FlowCytometer
+from FlowCyPy import Population, distribution
+from FlowCyPy.detector import Detector
+from FlowCyPy.units import ohm, megahertz, ampere, volt, kelvin, watt, microsecond, microvolt
+from FlowCyPy import EventCorrelator, peak_locator
+from FlowCyPy import GaussianBeam
+from FlowCyPy import NoiseSetting
+
+NoiseSetting.include_noises = False
+
+np.random.seed(3)
+
+source = GaussianBeam(
+    numerical_aperture=0.3 * AU,
+    wavelength=988 * nanometer,
+    optical_power=20 * milliwatt
+)
+
+
+flow_cell = FlowCell(
+    source=source,
+    flow_speed=7.56 * meter / second,
+    flow_area=(10 * micrometer) ** 2,
+    run_time=0.2 * millisecond
+)
+
+
+scatterer = ScattererCollection(medium_refractive_index=1.33 * RIU)  # Medium refractive index of 1.33 (water)
+
+lymphocyte = Population(
+    name='lymphocyte',
+    particle_count=200 * particle,
+    size=distribution.Normal(mean=14_000 * nanometer, std_dev=1000 * nanometer),
+    refractive_index=distribution.Normal(mean=1.39 * RIU, std_dev=0.001 * RIU)
+)
+
+
+monocyte = Population(
+    name='monocyte',
+    particle_count=200 * particle,
+    size=distribution.Normal(mean=23_000 * nanometer, std_dev=1000 * nanometer),
+    refractive_index=distribution.Normal(mean=1.39 * RIU, std_dev=0.001 * RIU)
+)
+
+
+scatterer.add_population(lymphocyte, monocyte)
+
+flow_cell.initialize(scatterer_collection=scatterer)
+
+scatterer.plot()
+
+
+detector_0 = Detector(
+    name='forward',
+    phi_angle=0 * degree,
+    numerical_aperture=.2 * AU,
+    responsitivity=1 * ampere / watt,
+    sampling_freq=60 * megahertz,
+    noise_level=0.0 * volt,
+    saturation_level=1600 * microvolt,
+    resistance=150 * ohm,
+    temperature=300 * kelvin,
+)
+
+
+detector_1 = Detector(
+    name='side',
+    phi_angle=90 * degree,
+    numerical_aperture=.2 * AU,
+    responsitivity=1 * ampere / watt,
+    sampling_freq=60 * megahertz,
+    noise_level=0.0 * volt,
+    saturation_level=1600 * microvolt,
+    resistance=150 * ohm,
+    temperature=300 * kelvin,
+)
+
+
+cytometer = FlowCytometer(
+    detectors=[detector_0, detector_1],
+    flow_cell=flow_cell
+)
+
+
+cytometer.run_coupling_analysis()
+
+cytometer.initialize_signal()
+
+cytometer.simulate_pulse()
+
+cytometer.plot.coupling_distribution(log_scale=True, equal_limits=True)

{flowcypy-0.5.7 → flowcypy-0.5.8}/docs/examples/density_plots/1_populations.py

@@ -60,6 +60,7 @@ flow_cell.initialize(scatterer_collection=scatterer)  # Link populations to flow
 scatterer._log_properties()               # Display population properties
 scatterer.plot()                         # Visualize the population distributions
 
+# %%
 # Add forward scatter detector
 detector_0 = Detector(
     name='forward',                         # Detector name: Forward scatter
@@ -106,7 +107,7 @@ cytometer.initialize_signal()
 cytometer.simulate_pulse()
 
 # Visualize the scatter signals from both detectors
-cytometer.plot()
+cytometer.plot.signals()
 
 # %%
 # Step 5: Analyzing Pulse Signals

{flowcypy-0.5.7 → flowcypy-0.5.8}/docs/examples/density_plots/2_populations.py

@@ -62,6 +62,7 @@ scatterer.plot()
 
 source.print_properties()  # Print the laser source properties
 
+# %%
 # Step 5: Configure Detectors
 # Side scatter detector
 detector_0 = Detector(
@@ -109,7 +110,7 @@ cytometer.initialize_signal()
 cytometer.simulate_pulse()
 
 # Plot the results from both detectors
-cytometer.plot()
+cytometer.plot.signals()
 
 # %%
 # Step 5: Analyzing Pulse Signals
@@ -122,7 +123,7 @@ algorithm = peak_locator.MovingAverage(
 detector_0.set_peak_locator(algorithm)
 detector_1.set_peak_locator(algorithm)
 
-cytometer.plot(add_peak_locator=True)
+cytometer.plot.signals(add_peak_locator=True)
 
 analyzer = EventCorrelator(cytometer=cytometer)
 

{flowcypy-0.5.7 → flowcypy-0.5.8}/docs/examples/density_plots/3_populations.py

@@ -64,6 +64,7 @@ flow_cell.initialize(scatterer_collection=scatterer)   # Link populations to flo
 scatterer._log_properties()               # Display population properties
 scatterer.plot()                           # Visualize the population distributions
 
+# %%
 # Step 4: Simulating the Flow Cytometry Experiment
 # Initialize the cytometer and configure detectors
 # Add forward scatter detector
@@ -106,7 +107,7 @@ cytometer.initialize_signal()
 cytometer.simulate_pulse()
 
 # Visualize the scatter signals from both detectors
-cytometer.plot()
+cytometer.plot.signals()
 
 # %%
 # Step 5: Analyzing Pulse Signals

{flowcypy-0.5.7 → flowcypy-0.5.8}/docs/examples/density_plots/custom_populations.py

@@ -73,6 +73,7 @@ flow_cell.initialize(scatterer_collection=scatterer)  # Link populations to flow
 scatterer._log_properties()                # Display population properties
 scatterer.plot()                           # Visualize the population distributions
 
+# %%
 # Step 4: Simulating the Flow Cytometry Experiment
 # Initialize the cytometer and configure detectors
 # Add forward scatter detector
@@ -115,7 +116,7 @@ cytometer.initialize_signal()
 cytometer.simulate_pulse()
 
 # Visualize the scatter signals from both detectors
-cytometer.plot()
+cytometer.plot.signals()
 
 # %%
 # Step 5: Analyzing Pulse Signals