bmtool 0.6.8.1__py3-none-any.whl → 0.6.8.3__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 +406,78 @@ 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: np.ndarray = None, lfp_signal: np.ndarray = None, spike_fs : float = None,
+                   lfp_fs: float = None, method: str = 'hilbert', freq_of_interest: float = None,
+                   lowcut: float = None, highcut: float = None,
+                   bandwidth: float = 2.0) -> tuple:
+    """
+    Calculate Phase-Phase Coupling (PPC1) between spike times and LFP signal. Based on https://www.sciencedirect.com/science/article/pii/S1053811910000959
+    
+    Parameters:
+    - spike_times: Array of spike times 
+    - lfp_signal: Local field potential time series
+    - spike_fs: Sampling frequency in Hz of the spike times only needed if spikes times and lfp has different fs
+    - lfp_fs : Sampling frequency in Hz of the LFP
+    - method: 'wavelet' or 'hilbert' to choose the phase extraction method
+    - freq_of_interest: Desired frequency for wavelet phase extraction
+    - lowcut, highcut: Cutoff frequencies for bandpass filtering (Hilbert method)
+    - bandwidth: Bandwidth parameter for the wavelet
+    
+    Returns:
+    - ppc1: Phase-Phase Coupling value
+    - spike_phases: Phases at spike times
+    """
+    
+    if spike_fs == None:
+        spike_fs = lfp_fs
+    # Convert spike times to sample indices
+    spike_times_seconds = spike_times / spike_fs
+
+    # Then convert from seconds to samples at the new sampling rate
+    spike_indices = np.round(spike_times_seconds * lfp_fs).astype(int)
+    
+    # Filter indices to ensure they're within bounds of the LFP signal
+    valid_indices = [idx for idx in spike_indices if 0 <= idx < len(lfp_signal)]
+    if len(valid_indices) <= 1:
+        return 0, np.array([])
+    
+    # Extract phase using the specified method
+    if method == 'wavelet':
+        if freq_of_interest is None:
+            raise ValueError("freq_of_interest must be provided for the wavelet method.")
+        
+        # Apply CWT to extract phase at the frequency of interest
+        lfp_complex = wavelet_filter(x=lfp_signal, freq=freq_of_interest, fs=lfp_fs, bandwidth=bandwidth)
+        instantaneous_phase = np.angle(lfp_complex)
+        
+    elif method == 'hilbert':
+        if lowcut is None or highcut is None:
+            print("Lowcut and/or highcut were not defined, signal will not be filtered and will just take Hilbert transform for PPC1 calculation")
+            filtered_lfp = lfp_signal
+        else:
+            # Bandpass filter the signal
+            filtered_lfp = butter_bandpass_filter(lfp_signal, lowcut, highcut, lfp_fs)
+        
+        # Get phase using the Hilbert transform
+        analytic_signal = signal.hilbert(filtered_lfp)
+        instantaneous_phase = np.angle(analytic_signal)
+        
+    else:
+        raise ValueError("Invalid method. Choose 'wavelet' or 'hilbert'.")
+    
+    # Get phases at spike times
+    spike_phases = instantaneous_phase[valid_indices]
+    
+    # Calculate PPC1
+    n = len(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

@@ -1012,6 +1012,8 @@ def plot_firing_rate_distribution(individual_stats: pd.DataFrame, groupby: Union
 
     return ax
   
+def plot_entrainment():
+    pass
     
 def plot_3d_positions(config=None, populations_list=None, group_by=None, title=None, save_file=None, subset=None):
     """

{bmtool-0.6.8.1.dist-info → bmtool-0.6.8.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bmtool
-Version: 0.6.8.1
+Version: 0.6.8.3
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 

{bmtool-0.6.8.1.dist-info → bmtool-0.6.8.3.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=YoI7StM9qeZqyRfFX4M7oUGFz50tXTDOMIUqjYozj9s,54066
+bmtool/bmplot.py,sha256=ymyrNBctZoglsNA28733mXzM_l4b_3JIchXkQa2V2XE,54099
 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=bCpxqhdH6r71yXyqAv_M7BMq4x75lO7bctyyQi6pqdU,18186
 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-0.6.8.1.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
-bmtool-0.6.8.1.dist-info/METADATA,sha256=YVdlvlptmCrgkau7KEk_HkbEi__QcX0bAxDwe4eExJM,20431
-bmtool-0.6.8.1.dist-info/WHEEL,sha256=tTnHoFhvKQHCh4jz3yCn0WPTYIy7wXx3CJtJ7SJGV7c,91
-bmtool-0.6.8.1.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
-bmtool-0.6.8.1.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
-bmtool-0.6.8.1.dist-info/RECORD,,
+bmtool-0.6.8.3.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
+bmtool-0.6.8.3.dist-info/METADATA,sha256=jT598Nn_w-_OrCzo7L0cW1wtrv-OKW2aIDhxAqXA2-Q,20431
+bmtool-0.6.8.3.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
+bmtool-0.6.8.3.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
+bmtool-0.6.8.3.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
+bmtool-0.6.8.3.dist-info/RECORD,,

{bmtool-0.6.8.1.dist-info → bmtool-0.6.8.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (77.0.1)
+Generator: setuptools (77.0.3)
 Root-Is-Purelib: true
 Tag: py3-none-any