Merge branch 'main' into get_centroid

.github/workflows/continuous-integration.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11']
         os: [ubuntu-latest]
     env:
       OS: ${{ matrix.os }}

plantcv/annotate/__init__.py

@@ -1,6 +1,10 @@
+from importlib.metadata import version
 from plantcv.annotate.classes import Points
 from plantcv.annotate.get_centroids import get_centroids
 
+# Auto versioning
+__version__ = version("plantcv-annotate")
+
 __all__ = [
     "Points",
     "get_centroids"

plantcv/annotate/classes.py

@@ -9,82 +9,49 @@
 from plantcv.plantcv import warn
 
 
-def _view(self, label="default", color="c", view_all=False):
-    """
-    View the label for a specific class label
-    Inputs:
-    label = (optional) class label, by default label="total"
-    color = desired color, by default color="c"
-    view_all = indicator of whether view all classes, by default view_all=False
-    :param label: string
-    :param color: string
-    :param view_all: boolean
-    :return:
-    """
-    if label not in self.coords and color in self.colors.values():
-        warn("The color assigned to the new class label is already used, if proceeding, "
-             "items from different classes will not be distinguishable in plots!")
-    if label is not None:
-        self.label = label
-    self.color = color
-    self.view_all = view_all
-
-    if label not in self.coords:
-        self.coords[self.label] = []
-        self.count[self.label] = 0
-    self.colors[self.label] = color
-
-    self.fig, self.ax = plt.subplots(1, 1, figsize=self.figsize)
-
-    self.events = []
-    self.fig.canvas.mpl_connect('button_press_event', self.onclick)
-
-    self.ax.imshow(cv2.cvtColor(self.img, cv2.COLOR_BGR2RGB))
-    self.ax.set_title("Please left click on objects\n Right click to remove")
-    self.p_not_current = 0
-    # if view_all is True, show all already marked markers
-    if view_all:
-        for k in self.coords:
-            for (x, y) in self.coords[k]:
-                self.ax.plot(x, y, marker='x', c=self.colors[k])
-                if self.label not in self.coords or len(self.coords[self.label]) == 0:
-                    self.p_not_current += 1
-    else:
-        for (x, y) in self.coords[self.label]:
-            self.ax.plot(x, y, marker='x', c=color)
-
-
 class Points:
     """Point annotation/collection class to use in Jupyter notebooks. It allows the user to
     interactively click to collect coordinates from an image. Left click collects the point and
-    right click removes the closest collected point
+    right click removes the closest collected point.
     """
 
-    def __init__(self, img, figsize=(12, 6), label="default"):
-        """Initialization
-        :param img: image data
-        :param figsize: desired figure size, (12,6) by default
-        :param label: current label for group of annotations, similar to pcv.params.sample_label
-        :attribute coords: list of points as (x,y) coordinates tuples
+    def __init__(self, img, figsize=(12, 6), label="default", color="r", view_all=False):
+        """Points initialization method.
+
+        Parameters
+        ----------
+        img : numpy.ndarray
+            image to annotate
+        figsize : tuple, optional
+            figure plotting size, by default (12, 6)
+        label : str, optional
+            class label, by default "default"
         """
         self.img = img
+        self.figsize = figsize
+        self.label = label  # current label
+        self.color = color  # current color
+        self.view_all = view_all  # a flag indicating whether or not view all labels
         self.coords = {}  # dictionary of all coordinates per group label
         self.events = []  # includes right and left click events
         self.count = {}  # a dictionary that saves the counts of different groups (labels)
-        self.label = label  # current label
         self.sample_labels = []  # list of all sample labels, one to one with points collected
-        self.view_all = None  # a flag indicating whether or not view all labels
-        self.color = None  # current color
         self.colors = {}  # all used colors
-        self.figsize = figsize
 
-        _view(self, label=label, color="r", view_all=True)
+        self.view(label=self.label, color=self.color, view_all=self.view_all)
 
     def onclick(self, event):
-        """Handle mouse click events."""
+        """Handle mouse click events
+
+        Parameters
+        ----------
+        event : matplotlib.backend_bases.MouseEvent
+            matplotlib MouseEvent object
+        """
+        print(type(event))
         self.events.append(event)
         if event.button == 1:
-
+            # Add point to the plot
             self.ax.plot(event.xdata, event.ydata, marker='x', c=self.color)
             self.coords[self.label].append((floor(event.xdata), floor(event.ydata)))
             self.count[self.label] += 1
@@ -99,43 +66,45 @@ def onclick(self, event):
             self.sample_labels.pop(idx_remove)
         self.fig.canvas.draw()
 
-    def print_coords(self, outfile):
+    def print_coords(self, filename):
         """Save collected coordinates to a file.
-        Input variables:
-        outfile = Name of the file to save collected coordinate
-        :param filename: str
-        :return:
+
+        Parameters
+        ----------
+        filename : str
+            output filename
         """
         # Open the file for writing
-        with open(outfile, "w") as fp:
+        with open(filename, "w") as fp:
             # Save the data in JSON format with indentation
             json.dump(obj=self.coords, fp=fp, indent=4)
 
     def import_list(self, coords, label="default"):
-        """Import center coordinates of already detected objects
-        Inputs:
-        coords = list of center coordinates of already detected objects.
-        label = class label for imported coordinates, by default label="default".
-        :param coords: list
-        :param label: string
-        :return:
+        """Import coordinates.
+
+        Parameters
+        ----------
+        coords : list
+            list of coordinates (tuples)
+        label : str, optional
+            class label, by default "default"
         """
         if label not in self.coords:
             self.coords[label] = []
-            for (y, x) in coords:
+            for (x, y) in coords:
                 self.coords[label].append((x, y))
             self.count[label] = len(self.coords[label])
-            _view(self, label=label, color=self.color, view_all=False)
+            self.view(label=label, color=self.color, view_all=False)
         else:
             warn(f"{label} already included and counted, nothing is imported!")
 
     def import_file(self, filename):
-        """Method to import coordinates from file to Points object
+        """Import coordinates from a file.
 
-        Inputs:
-        filename = filename of stored coordinates and classes
-        :param filename: str
-        :return:
+        Parameters
+        ----------
+        filename : str
+            JSON file containing Points annotations
         """
         with open(filename, "r") as fp:
             coords = json.load(fp)
@@ -147,16 +116,45 @@ def import_file(self, filename):
             keycoor = list(map(lambda sub: (sub[1], sub[0]), keycoor))
             self.import_list(keycoor, label=key)
 
-    def view(self, label="default", color="c", view_all=False):
-        """Method to view current annotations
-
-        Inputs:
-        label = (optional) class label, by default label="total"
-        color = desired color, by default color="c"
-        view_all = indicator of whether view all classes, by default view_all=False
-        :param label: string
-        :param color: string
-        :param view_all: boolean
-        :return:
+    def view(self, label="default", color="r", view_all=False):
+        """View coordinates for a specific class label.
+
+        Parameters
+        ----------
+        label : str, optional
+            class label, by default "default"
+        color : str, optional
+            marker color, by default "r"
+        view_all : bool, optional
+            view all classes or a single class, by default False
         """
-        _view(self, label=label, color=color, view_all=view_all)
+        if label not in self.coords and color in self.colors.values():
+            warn("The color assigned to the new class label is already used, if proceeding, "
+                 "items from different classes will not be distinguishable in plots!")
+        self.label = label
+        self.color = color
+        self.view_all = view_all
+
+        if self.label not in self.coords:
+            self.coords[self.label] = []
+            self.count[self.label] = 0
+        self.colors[self.label] = self.color
+
+        self.fig, self.ax = plt.subplots(1, 1, figsize=self.figsize)
+
+        self.events = []
+        self.fig.canvas.mpl_connect('button_press_event', self.onclick)
+
+        self.ax.imshow(cv2.cvtColor(self.img, cv2.COLOR_BGR2RGB))
+        self.ax.set_title("Please left click on objects\n Right click to remove")
+        self.p_not_current = 0
+        # if view_all is True, show all already marked markers
+        if self.view_all:
+            for k in self.coords:
+                for (x, y) in self.coords[k]:
+                    self.ax.plot(x, y, marker='x', c=self.colors[k])
+                    if self.label not in self.coords or len(self.coords[self.label]) == 0:
+                        self.p_not_current += 1
+        else:
+            for (x, y) in self.coords[self.label]:
+                self.ax.plot(x, y, marker='x', c=self.color)

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools >= 61.0"]
+requires = ["setuptools >= 64.0", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools.packages.find]
@@ -26,7 +26,15 @@ classifiers = [
     "Intended Audience :: Science/Research",
 ]
 
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "pytest-cov",
+]
+
 [project.urls]
 Homepage = "https://plantcv.org"
 Documentation = "https://plantcv.readthedocs.io"
 Repository = "https://github.com/danforthcenter/plantcv-annotate"
+
+[tool.setuptools_scm]

tests/test_annotate_points.py

@@ -72,7 +72,7 @@ def test_points_print_coords(test_data, tmpdir):
     drawer_rgb.onclick(e2)
 
     # Save collected coords out 
-    drawer_rgb.print_coords(outfile=filename)
+    drawer_rgb.print_coords(filename)
     assert os.path.exists(filename)
 
 def test_points_import_list(test_data):