bmtool 0.6.8__py3-none-any.whl → 0.6.8.2__py3-none-any.whl

bmtool/SLURM.py

@@ -305,6 +305,45 @@ export OUTPUT_DIR={case_output_dir}
         return True
 
 
+def get_relative_path(endpoint, absolute_path):
+    """Convert absolute path to relative path for Globus transfer."""
+    try:
+        # Get the directories at the mount point
+        result = subprocess.run(["globus", "ls", f"{endpoint}:/"], capture_output=True, text=True, check=True)
+        dirs = set(result.stdout.splitlines())  # Convert to a set for quicker lookup
+
+        # Split the absolute path into parts
+        path_parts = absolute_path.strip("/").split("/")
+
+        # Find the first matching directory in the list
+        for i, part in enumerate(path_parts):
+            if part+"/" in dirs:
+                # The mount point is everything up to and including this directory
+                mount_point = "/" + "/".join(path_parts[:i])
+                relative_path = absolute_path.replace(mount_point, "", 1).lstrip("/")
+                return relative_path
+        
+        print("Error: Could not determine relative path.")
+        return None
+    except subprocess.CalledProcessError as e:
+        print(f"Error retrieving directories from Globus: {e}")
+        return None
+
+def globus_transfer(source_endpoint, dest_endpoint, source_path, dest_path):
+    """
+    Transfers file using custom globus transfer function. 
+    For more info see https://github.com/GregGlickert/transfer-files/blob/main/globus_transfer.sh
+    """
+    relative_source_path = get_relative_path(source_endpoint, source_path)
+    if relative_source_path is None:
+        print("Transfer aborted: Could not determine relative source path.")
+        return
+    
+    command = f"globus transfer {source_endpoint}:{relative_source_path} {dest_endpoint}:{dest_path} --label 'bmtool slurm transfer'"
+    os.system(command)
+
+
+
 class BlockRunner:
     """
     Class to handle submitting multiple blocks sequentially.
@@ -334,6 +373,7 @@ class BlockRunner:
         Updates the JSON file with new parameters before each block run.
         """
         for i, block in enumerate(self.blocks):
+            print(block.output_base_dir)
             # Update JSON file with new parameter value
             if self.json_file_path == None and self.param_values == None:
                 source_dir = block.component_path

bmtool/analysis/lfp.py

@@ -406,3 +406,64 @@ def calculate_plv_over_time(x1: np.ndarray, x2: np.ndarray, fs: float,
     return np.array(plv_over_time), np.array(times)
 
 
+def calculate_ppc1(spike_times, lfp_signal, fs, freq_range, window_size=0.5):
+    """
+    Calculate PPC1 metric between spike times and LFP signal using the vector dot product method.
+    
+    Parameters:
+    -----------
+    spike_times : array_like
+        Array of spike times in seconds
+    lfp_signal : array_like
+        Local field potential time series
+    fs : float
+        Sampling frequency of the LFP signal in Hz
+    freq_range : tuple
+        Frequency range (low, high) to filter the LFP signal in Hz
+    window_size : float, optional
+        Size of the window around each spike in seconds, default is 0.5s
+    
+    Returns:
+    --------
+    ppc1 : float
+        PPC1 value
+    phases : array
+        Phases at spike times
+    """
+    # Convert spike times to sample indices
+    spike_indices = np.round(spike_times * fs).astype(int)
+    
+    # Filter LFP in the frequency band of interest
+    nyquist = fs / 2
+    b, a = signal.butter(3, [freq_range[0] / nyquist, freq_range[1] / nyquist], btype='band')
+    filtered_lfp = signal.filtfilt(b, a, lfp_signal)
+    
+    # Get analytic signal through Hilbert transform
+    analytic_signal = signal.hilbert(filtered_lfp)
+    
+    # Extract instantaneous phase
+    instantaneous_phase = np.angle(analytic_signal)
+    
+    # Get phases at spike times
+    spike_phases = []
+    for spike_idx in spike_indices:
+        if 0 <= spike_idx < len(instantaneous_phase):
+            spike_phases.append(instantaneous_phase[spike_idx])
+    
+    spike_phases = np.array(spike_phases)
+    
+    # Calculate PPC1
+    n = len(spike_phases)
+    if n <= 1:
+        return 0, spike_phases
+    
+    # Convert phases to unit vectors in the complex plane
+    unit_vectors = np.exp(1j * spike_phases)
+    
+    # Calculate the resultant vector
+    resultant_vector = np.sum(unit_vectors)
+    
+    # PPC1 is the squared length of the resultant vector divided by n²
+    ppc1 = (np.abs(resultant_vector) ** 2) / (n ** 2)
+    
+    return ppc1, spike_phases

bmtool/bmplot.py

@@ -1007,7 +1007,7 @@ def plot_firing_rate_distribution(individual_stats: pd.DataFrame, groupby: Union
     ax.set_xticklabels(ax.get_xticklabels(), rotation=45, ha="right")
     ax.set_xlabel("Population Group")
     ax.set_ylabel("Firing Rate (spikes/s)")
-    ax.set_title("Firing Rate Distribution by Population")
+    ax.set_title("Firing Rate Distribution for individual cells")
     ax.grid(axis='y', linestyle='--', alpha=0.7)
 
     return ax

{bmtool-0.6.8.dist-info → bmtool-0.6.8.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: bmtool
-Version: 0.6.8
+Version: 0.6.8.2
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 
@@ -31,6 +31,7 @@ Requires-Dist: pynmodlt
 Requires-Dist: xarray
 Requires-Dist: fooof
 Requires-Dist: requests
+Requires-Dist: pyyaml
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
@@ -38,6 +39,7 @@ Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
 Dynamic: license
+Dynamic: license-file
 Dynamic: requires-dist
 Dynamic: summary
 

{bmtool-0.6.8.dist-info → bmtool-0.6.8.2.dist-info}/RECORD

@@ -1,7 +1,7 @@
-bmtool/SLURM.py,sha256=AKxu_Ln9wuCBVLdOJP4yAN59jYt222DM-iUlsQojNvY,18145
+bmtool/SLURM.py,sha256=umHYGUX2HDlZr6Zo89wQekGrK9mZdAi0rBdCA7a--hE,19904
 bmtool/__init__.py,sha256=ZStTNkAJHJxG7Pwiy5UgCzC4KlhMS5pUNPtUJZVwL_Y,136
 bmtool/__main__.py,sha256=TmFkmDxjZ6250nYD4cgGhn-tbJeEm0u-EMz2ajAN9vE,650
-bmtool/bmplot.py,sha256=PJeciKP89o9dOCB3prTTeI7ZDNwUBYtbUSvAmjn1uOo,54059
+bmtool/bmplot.py,sha256=YoI7StM9qeZqyRfFX4M7oUGFz50tXTDOMIUqjYozj9s,54066
 bmtool/connectors.py,sha256=hWkUUcJ4tmas8NDOFPPjQT-TgTlPcpjuZsYyAW2WkPA,72242
 bmtool/graphs.py,sha256=K8BiughRUeXFVvAgo8UzrwpSClIVg7UfmIcvtEsEsk0,6020
 bmtool/manage.py,sha256=_lCU0qBQZ4jSxjzAJUd09JEetb--cud7KZgxQFbLGSY,657
@@ -9,7 +9,7 @@ bmtool/plot_commands.py,sha256=Tqujyf0c0u8olhiHOMwgUSJXIIE1hgjv6otb25G9cA0,12298
 bmtool/singlecell.py,sha256=XZAT_2n44EhwqVLnk3qur9aO7oJ-10axJZfwPBslM88,27219
 bmtool/synapses.py,sha256=gIkfLhKDG2dHHCVJJoKuQrFn_Qut843bfk_-s97wu6c,54553
 bmtool/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bmtool/analysis/lfp.py,sha256=Zp-aJ8x2KmsI3h_mqvq4u9ixFYu4n0CxQpgdbYnrtYE,14909
+bmtool/analysis/lfp.py,sha256=DXZvxYMVjFiCJS_IySQIUrpBQjdNuHVL8A7rxrHB7xo,16900
 bmtool/analysis/spikes.py,sha256=qqJ4zD8xfvSwltlWm_Bhicdngzl6uBqH6Kn5wOMKRc8,11507
 bmtool/debug/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/debug/commands.py,sha256=AwtcR7BUUheM0NxvU1Nu234zCdpobhJv5noX8x5K2vY,583
@@ -19,9 +19,9 @@ bmtool/util/commands.py,sha256=zJF-fiLk0b8LyzHDfvewUyS7iumOxVnj33IkJDzux4M,64396
 bmtool/util/util.py,sha256=00vOAwTVIifCqouBoFoT0lBashl4fCalrk8fhg_Uq4c,56654
 bmtool/util/neuron/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/util/neuron/celltuner.py,sha256=xSRpRN6DhPFz4q5buq_W8UmsD7BbUrkzYBEbKVloYss,87194
-bmtool-0.6.8.dist-info/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
-bmtool-0.6.8.dist-info/METADATA,sha256=KuVWM0W-zZpBGO8JF3y6etJw_bfyvG-F8-78fi-ORJ4,20385
-bmtool-0.6.8.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
-bmtool-0.6.8.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
-bmtool-0.6.8.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
-bmtool-0.6.8.dist-info/RECORD,,
+bmtool-0.6.8.2.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
+bmtool-0.6.8.2.dist-info/METADATA,sha256=pE_Li9uoVYndKge-Gcm7gawxW71VbGfFhEL1lT0-kB8,20431
+bmtool-0.6.8.2.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
+bmtool-0.6.8.2.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
+bmtool-0.6.8.2.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
+bmtool-0.6.8.2.dist-info/RECORD,,

{bmtool-0.6.8.dist-info → bmtool-0.6.8.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (76.0.0)
+Generator: setuptools (77.0.3)
 Root-Is-Purelib: true
 Tag: py3-none-any