bug fixes and reorganization

eyepy/core/config.py

@@ -0,0 +1,20 @@
+import seaborn as sns
+
+# Plotting config
+
+# PR1 and EZ map to 14 and PR2 and IZ map to 15. Hence both names can be used
+# to access the same data
+SEG_MAPPING = {"ILM": 0, "BM": 1, "RNFL": 2, "NFL": 2, "GCL": 3, "IPL": 4,
+               "INL": 5, "OPL": 6, "ONL": 7, "ELM": 8, "IOS": 9, "OPT": 10,
+               "CHO": 11, "VIT": 12, "ANT": 13, "EZ": 14, "PR1": 14, "IZ": 15,
+               "PR2": 15, "RPE": 16}
+
+# Line Style for Layers in B-Scan
+layers_kwargs = {"linewidth": 0.3, "linestyle": "-"}
+
+# Line Style for B-Scan positions on Slo
+line_kwargs = {"linewidth": 0.3, "linestyle": "-"}
+
+# Colors for different Layers
+color_palette = sns.color_palette("hls", 17)
+layers_color = {key: color_palette[value] for key, value in SEG_MAPPING.items()}

eyepy/core/octbase.py

@@ -0,0 +1,150 @@
+import warnings
+from abc import ABC, abstractmethod
+
+import numpy as np
+from matplotlib import pyplot as plt
+
+from eyepy.core import config
+
+
+class Oct(ABC):
+
+    @abstractmethod
+    def __getitem__(self, key):
+        raise NotImplementedError()
+
+    @abstractmethod
+    def __len__(self):
+        raise NotImplementedError()
+
+    @property
+    @abstractmethod
+    def slo(self):
+        raise NotImplementedError()
+
+    @property
+    @abstractmethod
+    def volume(self):
+        raise NotImplementedError()
+
+    @property
+    @abstractmethod
+    def volume_raw(self):
+        raise NotImplementedError()
+
+    @property
+    @abstractmethod
+    def segmentation(self):
+        raise NotImplementedError()
+
+    @property
+    @abstractmethod
+    def segmentation_raw(self):
+        raise NotImplementedError()
+
+    @property
+    @abstractmethod
+    def meta(self):
+        raise NotImplementedError()
+
+    def plot(self, ax=None, bscan_positions=None, line_kwargs=None):
+        """ Plot Slo with localization of corresponding B-Scans"""
+
+        if ax is None:
+            fig, ax = plt.subplots(1, 1)
+        else:
+            fig = plt.gcf()
+
+        if bscan_positions is None:
+            bscan_positions = []
+        elif bscan_positions == "all":
+            bscan_positions = range(0, len(self))
+
+        if line_kwargs is None:
+            line_kwargs = config.line_kwargs
+        else:
+            line_kwargs = {**config.line_kwargs, **line_kwargs}
+
+        ax.imshow(self.slo, cmap="gray")
+
+        for i in bscan_positions:
+            bscan = self[i]
+            ax.plot(np.array([bscan.StartX, bscan.EndX]) / bscan.ScaleXSlo,
+                    np.array([bscan.StartX, bscan.EndX]) / bscan.ScaleXSlo,
+                    **line_kwargs)
+
+    def plot_slo_bscan(self, ax=None, n_bscan=0):
+        """ Plot Slo with one selected B-Scan """
+        pass
+
+    def plot_bscans(self, bs_range=range(0, 8), cols=4, layers=None,
+                    layers_kwargs=None):
+        """ Plot a grid with B-Scans """
+        rows = int(np.ceil(len(bs_range) / cols))
+        if layers is None:
+            layers = []
+
+        fig, axes = plt.subplots(
+            cols, rows, figsize=(rows * 4, cols * 4))
+
+        with np.errstate(invalid='ignore'):
+            for i in bs_range:
+                bscan = self[i]
+                ax = axes.flatten()[i]
+                bscan.plot(ax=ax, layers=layers, layers_kwargs=layers_kwargs)
+
+
+class Bscan:
+
+    @property
+    @abstractmethod
+    def scan(self):
+        raise NotImplementedError()
+
+    @property
+    @abstractmethod
+    def scan_raw(self):
+        raise NotImplementedError()
+
+    @property
+    @abstractmethod
+    def segmentation(self):
+        raise NotImplementedError()
+
+    @property
+    @abstractmethod
+    def segmentation_raw(self):
+        raise NotImplementedError()
+
+    def plot(self, ax=None, layers=None, layers_kwargs=None, layers_color=None):
+        """ Plot B-Scan with segmented Layers """
+        if ax is None:
+            fig, ax = plt.subplots(1, 1)
+        else:
+            fig = plt.gcf()
+
+        if layers is None:
+            layers = []
+        elif layers == "all":
+            layers = config.SEG_MAPPING.keys()
+
+        if layers_kwargs is None:
+            layers_kwargs = config.layers_kwargs
+        else:
+            layers_kwargs = {**config.layers_kwargs, **layers_kwargs}
+
+        if layers_color is None:
+            layers_color = config.layers_color
+        else:
+            layers_color = {**config.layers_color, **layers_color}
+
+        ax.imshow(self.scan, cmap="gray")
+        for layer in layers:
+            color = layers_color[layer]
+            try:
+                segmentation = self.segmentation[layer]
+                ax.plot(segmentation, color=color,
+                        **layers_kwargs)
+            except KeyError:
+                warnings.warn(f"Layer '{layer}' has no Segmentation",
+                              UserWarning)

eyepy/io/__init__.py

@@ -1,3 +1,2 @@
 # -*- coding: utf-8 -*-
-from .he_vol import HeyexOct, read_vol
-from .he_xml import read_xml_export
+from .heyex.heyex import read_xml, read_vol, HeyexOct