UnitMatchPy 2.1__tar.gz → 2.2__tar.gz

UnitMatchPy-2.2/PKG-INFO

@@ -0,0 +1,40 @@
+Metadata-Version: 2.1
+Name: UnitMatchPy
+Version: 2.2
+Author: Enny van Beest, Celian Bimbard and Sam Dodgson
+Author-email: e.beest@ucl.ac.uk
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# Unit Match - Python
+
+## Run UMPy
+
+To run UMPy standard spike sorting data is needed; channel positions and 2 extracted raw waveforms for each unit. This can be calculated externally [BombCell](https://github.com/Julie-Fabre/bombcell) or using *extract_raw_demo.ipynb* to extract these waveforms from compressed data (.cbin and .ch) or raw data. There is also a [Spike Interface](https://spikeinterface.readthedocs.io/en/latest/) integrated notebook *UMPy_spike_interface_demo.ipynb* which uses spike interface to get this data.
+Be careful not to mix and match the different ways of extracting raw waveforms, as there are difference between the methods.
+
+There are to example notebooks for running UMPy *UMPy_example.ipynb* and *UMPy_example_detailed.ipynb*. These notebooks will guide you through running Unit Match all you need to supply is paths to the data. *UMPy_example.ipynb* is recommended to use first as it is simpler, however *UMPy_example_detailed.ipynb* may be useful in unique cases as it is more modular.
+
+The GUI is a optional step to curated and investigate the information Unit Match has calculated; for efficient usage of the GUI please look at *GUI_Reference_Guide.md* in the Demo Notebooks folder.
+
+## Dependencies
+
+This version relies on many core python packages: [numpy](https://numpy.org/), [scipy](https://scipy.org/), [JobLib](https://joblib.readthedocs.io/en/stable/), [pandas](https://pandas.pydata.org/), [tkinter](https://docs.python.org/3/library/tkinter.html) and [matplotlib](https://matplotlib.org/). All of these libaries come with a [Anaconda](https://www.anaconda.com/download/) version of python. 
+For extracting raw data, the library [mtscomp](https://github.com/int-brain-lab/mtscomp) is needed, and can be installed by `pip install mtscomp`.
+
+
+## Installation 
+
+After creating an python environment
+
+```
+conda create --name UnitMatch python 
+conda activate UnitMatch
+```
+
+You can install UnitMatchPy with pip. It will automatically install all the dependencies.
+
+```
+pip install UnitMatchPy
+```

UnitMatchPy-2.2/README.md

@@ -0,0 +1,31 @@
+# Unit Match - Python
+
+## Run UMPy
+
+To run UMPy standard spike sorting data is needed; channel positions and 2 extracted raw waveforms for each unit. This can be calculated externally [BombCell](https://github.com/Julie-Fabre/bombcell) or using *extract_raw_demo.ipynb* to extract these waveforms from compressed data (.cbin and .ch) or raw data. There is also a [Spike Interface](https://spikeinterface.readthedocs.io/en/latest/) integrated notebook *UMPy_spike_interface_demo.ipynb* which uses spike interface to get this data.
+Be careful not to mix and match the different ways of extracting raw waveforms, as there are difference between the methods.
+
+There are to example notebooks for running UMPy *UMPy_example.ipynb* and *UMPy_example_detailed.ipynb*. These notebooks will guide you through running Unit Match all you need to supply is paths to the data. *UMPy_example.ipynb* is recommended to use first as it is simpler, however *UMPy_example_detailed.ipynb* may be useful in unique cases as it is more modular.
+
+The GUI is a optional step to curated and investigate the information Unit Match has calculated; for efficient usage of the GUI please look at *GUI_Reference_Guide.md* in the Demo Notebooks folder.
+
+## Dependencies
+
+This version relies on many core python packages: [numpy](https://numpy.org/), [scipy](https://scipy.org/), [JobLib](https://joblib.readthedocs.io/en/stable/), [pandas](https://pandas.pydata.org/), [tkinter](https://docs.python.org/3/library/tkinter.html) and [matplotlib](https://matplotlib.org/). All of these libaries come with a [Anaconda](https://www.anaconda.com/download/) version of python. 
+For extracting raw data, the library [mtscomp](https://github.com/int-brain-lab/mtscomp) is needed, and can be installed by `pip install mtscomp`.
+
+
+## Installation 
+
+After creating an python environment
+
+```
+conda create --name UnitMatch python 
+conda activate UnitMatch
+```
+
+You can install UnitMatchPy with pip. It will automatically install all the dependencies.
+
+```
+pip install UnitMatchPy
+```

{UnitMatchPy-2.1 → UnitMatchPy-2.2}/UnitMatchPy/GUI.py

@@ -55,14 +55,17 @@ def run_GUI():
     not_match = []
     root = Tk()
     # downloaded theme from https://sourceforge.net/projects/tcl-awthemes/
-    theme_path = os.path.join(os.path.dirname(os.path.abspath(__file__)) , r'TkinterTheme\awthemes-10.4.0')
+    theme_path_rel = os.path.normpath(r'TkinterTheme\awthemes-10.4.0')
+    theme_path = os.path.join(os.path.dirname(os.path.abspath(__file__)) , theme_path_rel)
+
     root.tk.call('lappend', 'auto_path', theme_path)
     root.tk.call('package', 'require', 'awdark')
     s = ttk.Style(root)
     s.theme_use('awdark')
     root.title('UMPy - Manual Curation')
     #root.geometry('800x800')
-    root.iconbitmap(os.path.join(os.path.dirname(os.path.abspath(__file__)) , r'UM Logo.ico'))
+    icon = PhotoImage(file = os.path.join(os.path.dirname(os.path.abspath(__file__)) , 'GUI_icon.png'))
+    root.iconphoto(False, icon)
     background = ttk.Frame(root)
     background.place(x=0, y=0, relwidth=1.0, relheight=1.0)
 
@@ -909,7 +912,7 @@ def add_original_ID(UnitA, UnitB):
     if original_id_label.winfo_exists():
         original_id_label.destroy()
 
-    original_id_label = ttk.Label(root, text = f'The Original Unit IDs are:\nUnit A: {int(clus_info["original_id"][UnitA].squeeze())}   Unit B: {int(clus_info["original_id"][UnitB].squeeze())}', borderwidth = 2 , relief= 'groove')
+    original_id_label = ttk.Label(root, text = f'The Original Unit IDs are:\nUnit A: {int(clus_info["original_ids"][UnitA].squeeze())}   Unit B: {int(clus_info["original_ids"][UnitB].squeeze())}', borderwidth = 2 , relief= 'groove')
     original_id_label.grid( row = 0, column = 2, ipadx = 5, ipady = 5)
 
 

{UnitMatchPy-2.1 → UnitMatchPy-2.2}/UnitMatchPy/Save_utils.py

@@ -5,7 +5,7 @@ import numpy as np
 
 def make_match_table(scores_to_include, matches, output_prob, total_score, output_threshold, clus_info, param, UIDs = None, matches_curated = None):
     """
-    Creates the match table showing information for every pair of units
+    Creates the match table showing information for every pair of units.
 
     Parameters
     ----------
@@ -46,8 +46,8 @@ def make_match_table(scores_to_include, matches, output_prob, total_score, outpu
     unit_a_list = xx.reshape(n_units*n_units)
     unit_b_list = yy.reshape(n_units*n_units)
 
-    sessions_ids = clus_info['sessions_ids']
-    xx, yy = np.meshgrid(sessions_ids, sessions_ids)
+    session_id = clus_info['session_id']
+    xx, yy = np.meshgrid(session_id, session_id)
     unit_a_session_list = xx.reshape(n_units*n_units) + 1 # Add one here so it counts from one not 0
     unit_b_session_list = yy.reshape(n_units*n_units) + 1
 
@@ -442,8 +442,8 @@ def save_prob_for_phy(probability, param, clus_info):
         session_output = probability[session_switch[sid]:session_switch[sid+1], session_switch[sid]:session_switch[sid+1]]
         #If Only good units where used add values know to a matrix of NaNs 
         if session_switch[sid+1] - session_switch[sid] != n_units_per_session[sid]:
-            all_good_units = clus_info['GoodUnits'][sid].squeeze().astype(int)
-            for id, gid in enumerate(clus_info['GoodUnits'][sid].astype(int)):
+            all_good_units = clus_info['good_units'][sid].squeeze().astype(int)
+            for id, gid in enumerate(clus_info['good_units'][sid].astype(int)):
                 matrix_prob[gid, all_good_units] = session_output[id,:]
         else:
             matrix_prob = session_output

{UnitMatchPy-2.1 → UnitMatchPy-2.2}/UnitMatchPy/assign_unique_id.py

@@ -42,7 +42,7 @@ def assign_unique_id(output_prob_array, param, clus_info):
     List
         A list of arrays which gives each unit its group ID for each case
     """
-    all_cluster_ids = clus_info['original_id'] # each units has unique ID
+    all_cluster_ids = clus_info['original_ids'] # each units has unique ID
 
     #create arrays for the unique ids
     unique_id_liberal = np.arange(all_cluster_ids.shape[0])

{UnitMatchPy-2.1 → UnitMatchPy-2.2}/UnitMatchPy/utils.py

@@ -130,10 +130,12 @@ def load_good_waveforms(wave_paths, unit_label_paths, param, good_units_only = T
         if os.path.split(unit_label_paths[0])[1] == 'cluster_bc_unitType.tsv':
             unit_label = load_tsv(unit_label_paths[i])
             tmp_idx = np.array([s for s in unit_label if 'GOOD' in s or 'NON-SOMA GOOD' in s])[:,0].astype(np.int32)
+            tmp_idx = tmp_idx[:, np.newaxis] # keep the array shape consitant between different methodss
         else:
             unit_label = load_tsv(unit_label_paths[i])
             tmp_idx = np.argwhere(unit_label[:,1] == 'good')
 
+
         n_units_per_session_all.append(unit_label.shape[0])
         good_unit_idx = unit_label[tmp_idx, 0]
         good_units.append(good_unit_idx)
@@ -228,6 +230,7 @@ def get_good_units(unit_label_paths, good = True):
                 tmp_idx = np.array([s for s in unit_label if 'GOOD' in s or 'NON-SOMA GOOD' in s])[:,0].astype(np.int32)
             else:
                 tmp_idx = unit_label[:,0].astype(np.int32)
+            tmp_idx = tmp_idx[:, np.newaxis] # keep the array shape consitant between different methodss
         else:
             unit_label = load_tsv(unit_label_paths[i])
             if good == True:

UnitMatchPy-2.2/UnitMatchPy.egg-info/PKG-INFO

@@ -0,0 +1,40 @@
+Metadata-Version: 2.1
+Name: UnitMatchPy
+Version: 2.2
+Author: Enny van Beest, Celian Bimbard and Sam Dodgson
+Author-email: e.beest@ucl.ac.uk
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# Unit Match - Python
+
+## Run UMPy
+
+To run UMPy standard spike sorting data is needed; channel positions and 2 extracted raw waveforms for each unit. This can be calculated externally [BombCell](https://github.com/Julie-Fabre/bombcell) or using *extract_raw_demo.ipynb* to extract these waveforms from compressed data (.cbin and .ch) or raw data. There is also a [Spike Interface](https://spikeinterface.readthedocs.io/en/latest/) integrated notebook *UMPy_spike_interface_demo.ipynb* which uses spike interface to get this data.
+Be careful not to mix and match the different ways of extracting raw waveforms, as there are difference between the methods.
+
+There are to example notebooks for running UMPy *UMPy_example.ipynb* and *UMPy_example_detailed.ipynb*. These notebooks will guide you through running Unit Match all you need to supply is paths to the data. *UMPy_example.ipynb* is recommended to use first as it is simpler, however *UMPy_example_detailed.ipynb* may be useful in unique cases as it is more modular.
+
+The GUI is a optional step to curated and investigate the information Unit Match has calculated; for efficient usage of the GUI please look at *GUI_Reference_Guide.md* in the Demo Notebooks folder.
+
+## Dependencies
+
+This version relies on many core python packages: [numpy](https://numpy.org/), [scipy](https://scipy.org/), [JobLib](https://joblib.readthedocs.io/en/stable/), [pandas](https://pandas.pydata.org/), [tkinter](https://docs.python.org/3/library/tkinter.html) and [matplotlib](https://matplotlib.org/). All of these libaries come with a [Anaconda](https://www.anaconda.com/download/) version of python. 
+For extracting raw data, the library [mtscomp](https://github.com/int-brain-lab/mtscomp) is needed, and can be installed by `pip install mtscomp`.
+
+
+## Installation 
+
+After creating an python environment
+
+```
+conda create --name UnitMatch python 
+conda activate UnitMatch
+```
+
+You can install UnitMatchPy with pip. It will automatically install all the dependencies.
+
+```
+pip install UnitMatchPy
+```

{UnitMatchPy-2.1 → UnitMatchPy-2.2}/UnitMatchPy.egg-info/SOURCES.txt

@@ -4,6 +4,7 @@ README.md
 setup.py
 UnitMatchPy/Extract_raw_data.py
 UnitMatchPy/GUI.py
+UnitMatchPy/GUI_icon.png
 UnitMatchPy/Overlord.py
 UnitMatchPy/Save_utils.py
 UnitMatchPy/UM Logo.ico

{UnitMatchPy-2.1 → UnitMatchPy-2.2}/setup.py

@@ -5,7 +5,7 @@ with open('README.md', 'r') as f:
 
 setup(
     name="UnitMatchPy",
-    version="2.1",
+    version="2.2",
     descriptin="Description of the package",
     author="Enny van Beest, Celian Bimbard and Sam Dodgson",
     author_email="e.beest@ucl.ac.uk",

UnitMatchPy-2.1/PKG-INFO

@@ -1,38 +0,0 @@
-Metadata-Version: 2.1
-Name: UnitMatchPy
-Version: 2.1
-Author: Enny van Beest, Celian Bimbard and Sam Dodgson
-Author-email: e.beest@ucl.ac.uk
-Requires-Python: >=3.7
-Description-Content-Type: text/markdown
-License-File: LICENSE
-
-# Unit Match - Python
-
-## Run UMPy
-
-To run UMPy standard spike sorting data is needed; channel positions and 2 extractracted raw waveforms for each unit. This can be calculated exteranlly [BombCell](https://github.com/Julie-Fabre/bombcell) or using *ExtractRawDataDemo.ipynb* to extract these waveforms from compressed data (.cbin and .ch) or raw data. There is also a [Spike Interface](https://spikeinterface.readthedocs.io/en/latest/) intergrated notebook *UMPy_spike_interface_demo.ipynb* which uses spike interface to get this data.
-Be careful not to mix and match the different ways of exrtacting raw waveforms, as there are difference between the methods.
-
-There are to example notebooks for running UMPy *UMPyExample.ipynb* and *UMPyExampleBrief.ipynb*. These notebooks will guide you throuh running Unit Match all you need to supply is paths to the data. *UMPyExampleBried.ipynb* is reccomened to use first as it is simpler, however *UMPyExample.ipynb* may be useful in unique cases as it is more modular.
-
-The GUI is a optional step to curated and investigate the infomation Unit Match has calculated; for efficent usage of the GUI please look at *GUI_Reference_Guide.md* in the Demo Notebooks folder.
-## Dependencies
-This version relies on many core python packages [numpy](https://numpy.org/), [scipy](https://scipy.org/), [JobLib](https://joblib.readthedocs.io/en/stable/), [pandas](https://pandas.pydata.org/), [tkinter](https://docs.python.org/3/library/tkinter.html) and [matplotlib](https://matplotlib.org/). All of these libaries come with a [Anaconda](https://www.anaconda.com/download/) version of python. 
-For extracting raw data the library [mtscomp](https://github.com/int-brain-lab/mtscomp) is needed, this can be installed by `pip install mtscomp`.
-
-
-## Installation 
-
-After creating an python environment
-
-```
-conda create --name UnitMatch python 
-conda activate UnitMatch
-```
-
-You can install UnitMatchPy with pip. It will automatically install all the dependency.
-
-```
-pip install UnitMatchPy
-```

UnitMatchPy-2.1/README.md

@@ -1,29 +0,0 @@
-# Unit Match - Python
-
-## Run UMPy
-
-To run UMPy standard spike sorting data is needed; channel positions and 2 extractracted raw waveforms for each unit. This can be calculated exteranlly [BombCell](https://github.com/Julie-Fabre/bombcell) or using *ExtractRawDataDemo.ipynb* to extract these waveforms from compressed data (.cbin and .ch) or raw data. There is also a [Spike Interface](https://spikeinterface.readthedocs.io/en/latest/) intergrated notebook *UMPy_spike_interface_demo.ipynb* which uses spike interface to get this data.
-Be careful not to mix and match the different ways of exrtacting raw waveforms, as there are difference between the methods.
-
-There are to example notebooks for running UMPy *UMPyExample.ipynb* and *UMPyExampleBrief.ipynb*. These notebooks will guide you throuh running Unit Match all you need to supply is paths to the data. *UMPyExampleBried.ipynb* is reccomened to use first as it is simpler, however *UMPyExample.ipynb* may be useful in unique cases as it is more modular.
-
-The GUI is a optional step to curated and investigate the infomation Unit Match has calculated; for efficent usage of the GUI please look at *GUI_Reference_Guide.md* in the Demo Notebooks folder.
-## Dependencies
-This version relies on many core python packages [numpy](https://numpy.org/), [scipy](https://scipy.org/), [JobLib](https://joblib.readthedocs.io/en/stable/), [pandas](https://pandas.pydata.org/), [tkinter](https://docs.python.org/3/library/tkinter.html) and [matplotlib](https://matplotlib.org/). All of these libaries come with a [Anaconda](https://www.anaconda.com/download/) version of python. 
-For extracting raw data the library [mtscomp](https://github.com/int-brain-lab/mtscomp) is needed, this can be installed by `pip install mtscomp`.
-
-
-## Installation 
-
-After creating an python environment
-
-```
-conda create --name UnitMatch python 
-conda activate UnitMatch
-```
-
-You can install UnitMatchPy with pip. It will automatically install all the dependency.
-
-```
-pip install UnitMatchPy
-```

UnitMatchPy-2.1/UnitMatchPy.egg-info/PKG-INFO

@@ -1,38 +0,0 @@
-Metadata-Version: 2.1
-Name: UnitMatchPy
-Version: 2.1
-Author: Enny van Beest, Celian Bimbard and Sam Dodgson
-Author-email: e.beest@ucl.ac.uk
-Requires-Python: >=3.7
-Description-Content-Type: text/markdown
-License-File: LICENSE
-
-# Unit Match - Python
-
-## Run UMPy
-
-To run UMPy standard spike sorting data is needed; channel positions and 2 extractracted raw waveforms for each unit. This can be calculated exteranlly [BombCell](https://github.com/Julie-Fabre/bombcell) or using *ExtractRawDataDemo.ipynb* to extract these waveforms from compressed data (.cbin and .ch) or raw data. There is also a [Spike Interface](https://spikeinterface.readthedocs.io/en/latest/) intergrated notebook *UMPy_spike_interface_demo.ipynb* which uses spike interface to get this data.
-Be careful not to mix and match the different ways of exrtacting raw waveforms, as there are difference between the methods.
-
-There are to example notebooks for running UMPy *UMPyExample.ipynb* and *UMPyExampleBrief.ipynb*. These notebooks will guide you throuh running Unit Match all you need to supply is paths to the data. *UMPyExampleBried.ipynb* is reccomened to use first as it is simpler, however *UMPyExample.ipynb* may be useful in unique cases as it is more modular.
-
-The GUI is a optional step to curated and investigate the infomation Unit Match has calculated; for efficent usage of the GUI please look at *GUI_Reference_Guide.md* in the Demo Notebooks folder.
-## Dependencies
-This version relies on many core python packages [numpy](https://numpy.org/), [scipy](https://scipy.org/), [JobLib](https://joblib.readthedocs.io/en/stable/), [pandas](https://pandas.pydata.org/), [tkinter](https://docs.python.org/3/library/tkinter.html) and [matplotlib](https://matplotlib.org/). All of these libaries come with a [Anaconda](https://www.anaconda.com/download/) version of python. 
-For extracting raw data the library [mtscomp](https://github.com/int-brain-lab/mtscomp) is needed, this can be installed by `pip install mtscomp`.
-
-
-## Installation 
-
-After creating an python environment
-
-```
-conda create --name UnitMatch python 
-conda activate UnitMatch
-```
-
-You can install UnitMatchPy with pip. It will automatically install all the dependency.
-
-```
-pip install UnitMatchPy
-```