boris-behav-obs 9.4.1__py2.py3-none-any.whl → 9.5.2__py2.py3-none-any.whl

boris/plot_spectrogram_rt.py

@@ -24,10 +24,10 @@ Copyright 2012-2025 Olivier Friard
 import wave
 import matplotlib
 
-matplotlib.use("Qt5Agg")
+matplotlib.use("QtAgg")
 
 import numpy as np
-
+from scipy import signal
 from . import config as cfg
 
 from PySide6.QtWidgets import (
@@ -43,8 +43,6 @@ from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.figure import Figure
 import matplotlib.ticker as mticker
 
-# matplotlib.pyplot.switch_backend("Qt5Agg")
-
 
 class Plot_spectrogram_RT(QWidget):
     # send keypress event to mainwindow
@@ -115,7 +113,7 @@ class Plot_spectrogram_RT(QWidget):
         else:
             return False
 
-    def get_wav_info(self, wav_file: str):
+    def get_wav_info(self, wav_file: str) -> tuple[np.array, int]:
         """
         read wav file and extract information
 
@@ -184,7 +182,7 @@ class Plot_spectrogram_RT(QWidget):
 
         return {"media_length": self.media_length, "frame_rate": self.frame_rate}
 
-    def plot_spectro(self, current_time: float, force_plot: bool = False):
+    def plot_spectro(self, current_time: float, force_plot: bool = False) -> tuple[float, bool]:
         """
         plot sound spectrogram centered on the current time
 
@@ -200,15 +198,36 @@ class Plot_spectrogram_RT(QWidget):
 
         self.ax.clear()
 
+        window_type = "blackmanharris"  # self.config_param.get(cfg.SPECTROGRAM_WINDOW_TYPE, cfg.SPECTROGRAM_DEFAULT_WINDOW_TYPE)
+        nfft = int(self.config_param.get(cfg.SPECTROGRAM_NFFT, cfg.SPECTROGRAM_DEFAULT_NFFT))
+        noverlap = self.config_param.get(cfg.SPECTROGRAM_NOVERLAP, cfg.SPECTROGRAM_DEFAULT_NOVERLAP)
+        vmin = self.config_param.get(cfg.SPECTROGRAM_VMIN, cfg.SPECTROGRAM_DEFAULT_VMIN)
+        vmax = self.config_param.get(cfg.SPECTROGRAM_VMAX, cfg.SPECTROGRAM_DEFAULT_VMAX)
+
         # start
         if current_time <= self.interval / 2:
             self.ax.specgram(
-                self.sound_info[: int((self.interval) * self.frame_rate)],
+                self.sound_info[: int(self.interval * self.frame_rate)],
                 mode="psd",
-                # NFFT=1024,
+                NFFT=nfft,
                 Fs=self.frame_rate,
-                # noverlap=900,
+                noverlap=noverlap,
+                window=signal.get_window(window_type, nfft),
+                # matplotlib.mlab.window_hanning
+                # if window_type == "hanning"
+                # else matplotlib.mlab.window_hamming
+                # if window_type == "hamming"
+                # else matplotlib.mlab.window_blackmanharris
+                # if window_type == "blackmanharris"
+                # else matplotlib.mlab.window_hanning,
                 cmap=self.spectro_color_map,
+                vmin=vmin,
+                vmax=vmax,
+                # mode="psd",
+                ## NFFT=1024,
+                # Fs=self.frame_rate,
+                ## noverlap=900,
+                # cmap=self.spectro_color_map,
             )
 
             self.ax.set_xlim(current_time - self.interval / 2, current_time + self.interval / 2)
@@ -222,10 +241,25 @@ class Plot_spectrogram_RT(QWidget):
             self.ax.specgram(
                 self.sound_info[i:],
                 mode="psd",
-                # NFFT=1024,
+                NFFT=nfft,
                 Fs=self.frame_rate,
-                # noverlap=900,
+                noverlap=noverlap,
+                window=signal.get_window(window_type, nfft),
+                # matplotlib.mlab.window_hanning
+                # if window_type == "hanning"
+                # else matplotlib.mlab.window_hamming
+                # if window_type == "hamming"
+                # else matplotlib.mlab.window_blackmanharris
+                # if window_type == "blackmanharris"
+                # else matplotlib.mlab.window_hanning,
                 cmap=self.spectro_color_map,
+                vmin=vmin,
+                vmax=vmax,
+                # mode="psd",
+                ## NFFT=1024,
+                # Fs=self.frame_rate,
+                ## noverlap=900,
+                # cmap=self.spectro_color_map,
             )
 
             lim1 = current_time - (self.media_length - self.interval / 2)
@@ -248,10 +282,25 @@ class Plot_spectrogram_RT(QWidget):
                     )
                 ],
                 mode="psd",
-                # NFFT=1024,
+                NFFT=nfft,
                 Fs=self.frame_rate,
-                # noverlap=900,
+                noverlap=noverlap,
+                window=signal.get_window(window_type, nfft),
+                # matplotlib.mlab.window_hanning
+                # if window_type == "hanning"
+                # else matplotlib.mlab.window_hamming
+                # if window_type == "hamming"
+                # else matplotlib.mlab.window_blackmanharris
+                # if window_type == "blackmanharris"
+                # else matplotlib.mlab.window_hanning,
                 cmap=self.spectro_color_map,
+                vmin=vmin,
+                vmax=vmax,
+                # mode="psd",
+                ## NFFT=1024,
+                # Fs=self.frame_rate,
+                ## noverlap=900,
+                # cmap=self.spectro_color_map,
             )
 
             self.ax.xaxis.set_major_locator(mticker.FixedLocator(self.ax.get_xticks().tolist()))

boris/plot_waveform_rt.py

@@ -25,7 +25,7 @@ import wave
 from . import config as cfg
 import matplotlib
 
-matplotlib.use("Qt5Agg")
+matplotlib.use("QtAgg")
 
 import numpy as np
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QHBoxLayout, QPushButton, QLabel

boris/plugins.py

@@ -47,12 +47,12 @@ def add_plugins_to_menu(self):
         self.menu_plugins.addAction(action)
 
 
-def get_plugin_name(plugin_path: str):
+def get_plugin_name(plugin_path: str) -> str | None:
     """
-    get name of plugin
+    get name of a Python plugin
     """
     # search plugin name
-    plugin_name = None
+    plugin_name: str | None = None
     with open(plugin_path, "r") as f_in:
         for line in f_in:
             if line.startswith("__plugin_name__"):
@@ -61,6 +61,48 @@ def get_plugin_name(plugin_path: str):
     return plugin_name
 
 
+def get_r_plugin_name(plugin_path: str) -> str | None:
+    """
+    get name of a R plugin
+    """
+    # search plugin name
+    plugin_name: str | None = None
+    with open(plugin_path, "r") as f_in:
+        for line in f_in:
+            if line.startswith("plugin_name"):
+                if "=" in line:
+                    plugin_name = line.split("=")[1].strip().replace('"', "").replace("'", "")
+                    break
+                elif "<-" in line:
+                    plugin_name = line.split("<-")[1].strip().replace('"', "").replace("'", "")
+                    break
+                else:
+                    plugin_name = None
+                    break
+    return plugin_name
+
+
+def get_r_plugin_description(plugin_path: str) -> str | None:
+    """
+    get description of a R plugin
+    """
+    # search plugin name
+    plugin_description: str | None = None
+    with open(plugin_path, "r") as f_in:
+        for line in f_in:
+            if line.startswith("description"):
+                if "=" in line:
+                    plugin_description = line.split("=")[1].strip().replace('"', "").replace("'", "")
+                    break
+                elif "<-" in line:
+                    plugin_description = line.split("<-")[1].strip().replace('"', "").replace("'", "")
+                    break
+                else:
+                    plugin_description = None
+                    break
+    return plugin_description
+
+
 def load_plugins(self):
     """
     load selected plugins in analysis menu
@@ -80,8 +122,6 @@ def load_plugins(self):
 
     # load BORIS plugins
     for file_ in sorted((Path(__file__).parent / "analysis_plugins").glob("*.py")):
-        if file_.name == "__init__.py":
-            continue
         if file_.name.startswith("_"):
             continue
         plugin_name = get_plugin_name(file_)
@@ -96,8 +136,6 @@ def load_plugins(self):
     # load personal plugins
     if self.config_param.get(cfg.PERSONAL_PLUGINS_DIR, ""):
         for file_ in sorted(Path(self.config_param.get(cfg.PERSONAL_PLUGINS_DIR, "")).glob("*.py")):
-            if file_.name == "__init__.py":
-                continue
             if file_.name.startswith("_"):
                 continue
             plugin_name = get_plugin_name(file_)
@@ -109,6 +147,20 @@ def load_plugins(self):
 
                 self.config_param[cfg.ANALYSIS_PLUGINS][plugin_name] = str(file_)
 
+    # load personal R plugins
+    if self.config_param.get(cfg.PERSONAL_PLUGINS_DIR, ""):
+        for file_ in sorted(Path(self.config_param.get(cfg.PERSONAL_PLUGINS_DIR, "")).glob("*.R")):
+            if file_.name.startswith("_"):
+                continue
+            plugin_name = get_r_plugin_name(file_)
+            if plugin_name is not None and plugin_name not in self.config_param.get(cfg.EXCLUDED_PLUGINS, set()):
+                # check if plugin with same name already loaded
+                if plugin_name in self.config_param[cfg.ANALYSIS_PLUGINS]:
+                    msg()
+                    continue
+
+                self.config_param[cfg.ANALYSIS_PLUGINS][plugin_name] = str(file_)
+
     logging.debug(f"{self.config_param.get(cfg.ANALYSIS_PLUGINS, {})=}")
 
 
@@ -203,7 +255,7 @@ def run_plugin(self, plugin_name):
         QMessageBox.critical(self, cfg.programName, f"Plugin '{plugin_name}' not found")
         return
 
-    plugin_path = self.config_param.get(cfg.ANALYSIS_PLUGINS, {})[plugin_name]
+    plugin_path: str = self.config_param.get(cfg.ANALYSIS_PLUGINS, {}).get(plugin_name, "")
 
     logging.debug(f"{plugin_path=}")
 
@@ -213,24 +265,12 @@ def run_plugin(self, plugin_name):
 
     logging.debug(f"run plugin from {plugin_path}")
 
-    module_name = Path(plugin_path).stem
-
-    spec = importlib.util.spec_from_file_location(module_name, plugin_path)
-    plugin_module = importlib.util.module_from_spec(spec)
-
-    logging.debug(f"{plugin_module=}")
-
-    spec.loader.exec_module(plugin_module)
-
-    logging.info(
-        f"{plugin_module.__plugin_name__} loaded v.{getattr(plugin_module, '__version__')} v. {getattr(plugin_module, '__version_date__')}"
-    )
-
+    # select observations to analyze
     selected_observations, parameters = self.obs_param()
     if not selected_observations:
         return
 
-    logging.info("preparing dtaaframe for plugin")
+    logging.info("preparing dataframe for plugin")
 
     df = project_functions.project2dataframe(self.pj, selected_observations)
 
@@ -247,8 +287,79 @@ def run_plugin(self, plugin_name):
     filtered_df = plugin_df_filter(df, observations_list=selected_observations, parameters=parameters)
     logging.info("done")
 
-    plugin_results = plugin_module.run(filtered_df)
-    # test if plugin_tests is a tuple: if not transform to tuple
+    if Path(plugin_path).suffix == ".py":
+        # load plugin as module
+        module_name = Path(plugin_path).stem
+
+        spec = importlib.util.spec_from_file_location(module_name, plugin_path)
+        plugin_module = importlib.util.module_from_spec(spec)
+
+        logging.debug(f"{plugin_module=}")
+
+        spec.loader.exec_module(plugin_module)
+
+        plugin_version = plugin_module.__version__
+        plugin_version_date = plugin_module.__version_date__
+
+        logging.info(
+            f"{plugin_module.__plugin_name__} loaded v.{getattr(plugin_module, '__version__')} v. {getattr(plugin_module, '__version_date__')}"
+        )
+
+        # run plugin
+        plugin_results = plugin_module.run(filtered_df)
+
+    if Path(plugin_path).suffix in (".R", ".r"):
+        try:
+            from rpy2 import robjects
+            from rpy2.robjects import pandas2ri
+            from rpy2.robjects.packages import SignatureTranslatedAnonymousPackage
+            from rpy2.robjects.conversion import localconverter
+        except Exception:
+            QMessageBox.critical(self, cfg.programName, "The rpy2 Python module is not installed. R plugins cannot be used")
+            return
+
+        # Read code from file
+        try:
+            with open(plugin_path, "r") as f:
+                r_code = f.read()
+        except Exception:
+            QMessageBox.critical(self, cfg.programName, f"Error reading the plugin {plugin_path}.")
+            return
+
+        # read version
+        plugin_version = next(
+            (
+                x.split("<-")[1].replace('"', "").replace("'", "").strip()
+                for x in r_code.splitlines()
+                if x.replace(" ", "").startswith("version<-")
+            ),
+            None,
+        )
+        # read version date
+        plugin_version_date = next(
+            (
+                x.split("<-")[1].replace('"', "").replace("'", "").strip()
+                for x in r_code.split("\n")
+                if x.replace(" ", "").startswith("version_date<")
+            ),
+            None,
+        )
+
+        r_plugin = SignatureTranslatedAnonymousPackage(r_code, "r_plugin")
+
+        with localconverter(robjects.default_converter + pandas2ri.converter):
+            r_df = robjects.conversion.py2rpy(filtered_df)
+
+        try:
+            r_result = r_plugin.run(r_df)
+        except Exception as e:
+            QMessageBox.critical(self, cfg.programName, f"Error in the plugin {plugin_path}: {e}.")
+            return
+
+        with localconverter(robjects.default_converter + pandas2ri.converter):
+            plugin_results = robjects.conversion.rpy2py(r_result)
+
+    # test if plugin_results is a tuple: if not transform it to tuple
     if not isinstance(plugin_results, tuple):
         plugin_results = tuple([plugin_results])
 
@@ -261,7 +372,7 @@ def run_plugin(self, plugin_name):
             self.plugin_visu[-1].ptText.appendPlainText(result)
             self.plugin_visu[-1].show()
         elif isinstance(result, pd.DataFrame):
-            self.plugin_visu.append(view_df.View_df(plugin_name, f"{plugin_module.__version__} ({plugin_module.__version_date__})", result))
+            self.plugin_visu.append(view_df.View_df(plugin_name, f"{plugin_version} ({plugin_version_date})", result))
             self.plugin_visu[-1].show()
         else:
             # result is not str nor dataframe