Modularize Frontend

src/guppy/analysis/io_utils.py

@@ -6,17 +6,10 @@
 
 import h5py
 import numpy as np
-import pandas as pd
-
-logger = logging.getLogger(__name__)
 
+from ..utils.utils import takeOnlyDirs
 
-def takeOnlyDirs(paths):
-    removePaths = []
-    for p in paths:
-        if os.path.isfile(p):
-            removePaths.append(p)
-    return list(set(paths) - set(removePaths))
+logger = logging.getLogger(__name__)
 
 
 # find files by ignoring the case sensitivity
@@ -143,20 +136,6 @@ def get_coords(filepath, name, tsNew, removeArtifacts):  # TODO: Make less redun
     return coords
 
 
-def get_all_stores_for_combining_data(folderNames):
-    op = []
-    for i in range(100):
-        temp = []
-        match = r"[\s\S]*" + "_output_" + str(i)
-        for j in folderNames:
-            temp.append(re.findall(match, j))
-        temp = sorted(list(np.concatenate(temp).flatten()), key=str.casefold)
-        if len(temp) > 0:
-            op.append(temp)
-
-    return op
-
-
 # for combining data, reading storeslist file from both data and create a new storeslist array
 def check_storeslistfile(folderNames):
     storesList = np.array([[], []])
@@ -197,19 +176,6 @@ def get_control_and_signal_channel_names(storesList):
     return channels_arr
 
 
-# function to read h5 file and make a dataframe from it
-def read_Df(filepath, event, name):
-    event = event.replace("\\", "_")
-    event = event.replace("/", "_")
-    if name:
-        op = os.path.join(filepath, event + "_{}.h5".format(name))
-    else:
-        op = os.path.join(filepath, event + ".h5")
-    df = pd.read_hdf(op, key="df", mode="r")
-
-    return df
-
-
 def make_dir_for_cross_correlation(filepath):
     op = os.path.join(filepath, "cross_correlation_output")
     if not os.path.exists(op):

src/guppy/analysis/psth_average.py

@@ -10,10 +10,10 @@
 from .io_utils import (
     make_dir_for_cross_correlation,
     makeAverageDir,
-    read_Df,
     write_hdf5,
 )
 from .psth_utils import create_Df_for_psth, getCorrCombinations
+from ..utils.utils import read_Df
 
 logger = logging.getLogger(__name__)
 

src/guppy/analysis/standard_io.py

@@ -331,3 +331,18 @@ def read_freq_and_amp_from_hdf5(filepath, name):
     df = pd.read_hdf(op, key="df", mode="r")
 
     return df
+
+
+def write_transients_to_hdf5(filepath, name, z_score, ts, peaksInd):
+    event = f"transient_outputs_{name}"
+    write_hdf5(z_score, event, filepath, "z_score")
+    write_hdf5(ts, event, filepath, "timestamps")
+    write_hdf5(peaksInd, event, filepath, "peaksInd")
+
+
+def read_transients_from_hdf5(filepath, name):
+    event = f"transient_outputs_{name}"
+    z_score = read_hdf5(event, filepath, "z_score")
+    ts = read_hdf5(event, filepath, "timestamps")
+    peaksInd = read_hdf5(event, filepath, "peaksInd")
+    return z_score, ts, peaksInd

src/guppy/frontend/artifact_removal.py

@@ -0,0 +1,75 @@
+import logging
+import os
+
+import matplotlib.pyplot as plt
+import numpy as np
+
+from ..visualization.preprocessing import visualize_control_signal_fit
+
+logger = logging.getLogger(__name__)
+
+# Only set matplotlib backend if not in CI environment
+if not os.getenv("CI"):
+    plt.switch_backend("TKAgg")
+
+
+class ArtifactRemovalWidget:
+
+    def __init__(self, filepath, x, y1, y2, y3, plot_name, removeArtifacts):
+        self.coords = []  # List to store selected coordinates
+        self.filepath = filepath
+        self.plot_name = plot_name
+
+        if (y1 == 0).all() == True:
+            y1 = np.zeros(x.shape[0])
+
+        coords_path = os.path.join(filepath, "coordsForPreProcessing_" + plot_name[0].split("_")[-1] + ".npy")
+        artifacts_have_been_removed = removeArtifacts and os.path.exists(coords_path)
+        name = os.path.basename(filepath)
+        self.fig, self.ax1, self.ax2, self.ax3 = visualize_control_signal_fit(
+            x, y1, y2, y3, plot_name, name, artifacts_have_been_removed
+        )
+
+        self.cid = self.fig.canvas.mpl_connect("key_press_event", self._on_key_press)
+        self.fig.canvas.mpl_connect("close_event", self._on_close)
+
+    def _on_key_press(self, event):
+        """Handle key press events for artifact selection.
+
+        Pressing 'space' draws a vertical line at the cursor position to mark artifact boundaries.
+        Pressing 'd' removes the most recently added line.
+        """
+        if event.key == " ":
+            ix, iy = event.xdata, event.ydata
+            logger.info(f"x = {ix}, y = {iy}")
+            self.ax1.axvline(ix, c="black", ls="--")
+            self.ax2.axvline(ix, c="black", ls="--")
+            self.ax3.axvline(ix, c="black", ls="--")
+
+            self.fig.canvas.draw()
+
+            self.coords.append((ix, iy))
+
+            return self.coords
+
+        elif event.key == "d":
+            if len(self.coords) > 0:
+                logger.info(f"x = {self.coords[-1][0]}, y = {self.coords[-1][1]}; deleted")
+                del self.coords[-1]
+                self.ax1.lines[-1].remove()
+                self.ax2.lines[-1].remove()
+                self.ax3.lines[-1].remove()
+                self.fig.canvas.draw()
+
+            return self.coords
+
+    def _on_close(self, _event):
+        """Handle figure close event by saving coordinates and cleaning up."""
+        if self.coords and len(self.coords) > 0:
+            name_1 = self.plot_name[0].split("_")[-1]
+            np.save(os.path.join(self.filepath, "coordsForPreProcessing_" + name_1 + ".npy"), self.coords)
+            logger.info(
+                f"Coordinates file saved at {os.path.join(self.filepath, 'coordsForPreProcessing_'+name_1+'.npy')}"
+            )
+        self.fig.canvas.mpl_disconnect(self.cid)
+        self.coords = []

src/guppy/frontend/frontend_utils.py

@@ -0,0 +1,19 @@
+import logging
+import socket
+from random import randint
+
+logger = logging.getLogger(__name__)
+
+
+def scanPortsAndFind(start_port=5000, end_port=5200, host="127.0.0.1"):
+    while True:
+        port = randint(start_port, end_port)
+        sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+        sock.settimeout(0.001)  # Set timeout to avoid long waiting on closed ports
+        result = sock.connect_ex((host, port))
+        if result == 0:  # If the connection is successful, the port is open
+            continue
+        else:
+            break
+
+    return port