Started plotting module

choderalab · Nov 29, 2024 · 465a49d · 465a49d
2 parents 5a0fe45 + 5d9ebee
commit 465a49d
Showing 1 changed file with 35 additions and 13 deletions.
diff --git a/fluorescence_assay/plotting.py b/fluorescence_assay/plotting.py
@@ -1,27 +1,35 @@
 """Module to plot parsed plate reader ouptputs."""
 
+from abc import ABC, abstractmethod
+from dataclasses import dataclass, field
+from typing import Optional
+
 import matplotlib
 import matplotlib.pyplot as plt
 import numpy as np
 
-from .plate_reader import Measurements, IControlXML
-
-from abc import ABC, abstractmethod
-from dataclasses import dataclass, field
-from typing import Optional
+from .plate_reader import IControlXML, Measurements
 
 
 @dataclass
 class Plot(ABC):
     """"""
-    
+
     @abstractmethod
     def load_data(self, Measurement: Measurements, *args, **kwargs) -> None:
         """"""
         ...
 
-    def format_plot(self, axes: matplotlib.axes._axes.Axes, xlim: Optional[list[float]] = None, ylim: Optional[list[float]] = None, xlabel: Optional[str] = None, ylabel: Optional[str] = None, square: Optional[bool] = False):
-
+    def format_plot(
+        self,
+        axes: matplotlib.axes._axes.Axes,
+        xlim: Optional[list[float]] = None,
+        ylim: Optional[list[float]] = None,
+        xlabel: Optional[str] = None,
+        ylabel: Optional[str] = None,
+        square: Optional[bool] = False,
+    ):
+
         if xlim is not None:
             axes.set_xlim(xlim)
 
@@ -38,27 +46,41 @@ def format_plot(self, axes: matplotlib.axes._axes.Axes, xlim: Optional[list[floa
             axes.set_box_aspect(1)
 
 
-
 @dataclass
 class IControlXMLPlot(Plot):
     """"""
 
     _plate_read: dict = field(default_factory=dict, init=False)
 
     def load_data(self, IControlXML: IControlXML) -> None:
-        
+
         self._plate_read = IControlXML
 
     def get_wavelength_axis(self, section) -> np.ndarray:
 
-        lmin, lmax, lstep = [self._plate_read.get_parameter(section, parameter) for parameter in ["Emission Wavelength Start", "Emission Wavelength End", "Emission Wavelength Step Size"]]
+        lmin, lmax, lstep = (
+            self._plate_read.get_parameter(section, parameter)
+            for parameter in [
+                "Emission Wavelength Start",
+                "Emission Wavelength End",
+                "Emission Wavelength Step Size",
+            ]
+        )
 
         return np.arange(lmin, lmax + lstep, lstep)
 
-    def plot_well_spectrum(self, axes: matplotlib.axes._axes.Axes, section: str, well: str, cycle: Optional[int] = 1, color: Optional[tuple] = (0,0,0), label: Optional[str] = None) -> None:
+    def plot_well_spectrum(
+        self,
+        axes: matplotlib.axes._axes.Axes,
+        section: str,
+        well: str,
+        cycle: Optional[int] = 1,
+        color: Optional[tuple] = (0, 0, 0),
+        label: Optional[str] = None,
+    ) -> None:
 
         data = np.array(list(self._plate_read.get_well(section, well, cycle).values()))
 
         ll = self.get_wavelength_axis(section)
 
-        axes.plot(ll, data, color=color, label=label)
+        axes.plot(ll, data, color=color, label=label)