UnitMatchPy 2.11__tar.gz → 2.12a0__tar.gz

{UnitMatchPy-2.11/UnitMatchPy.egg-info → UnitMatchPy-2.12a0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: UnitMatchPy
-Version: 2.11
+Version: 2.12a0
 Author: Enny van Beest, Celian Bimbard and Sam Dodgson
 Author-email: e.beest@ucl.ac.uk
 Requires-Python: >=3.7
@@ -11,12 +11,12 @@ License-File: LICENSE
 
 ## 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.
+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 *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.
+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 infomation Unit Match has calculated; for efficent usage of the GUI please look at *GUI_Reference_Guide.md* in the Demo Notebooks folder.
+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, this can be installed by `pip install mtscomp`.

UnitMatchPy-2.12a0/README.md

@@ -0,0 +1,29 @@
+# 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, 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-2.11 → UnitMatchPy-2.12a0}/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)
@@ -228,7 +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 methods
+            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-2.11 → UnitMatchPy-2.12a0/UnitMatchPy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: UnitMatchPy
-Version: 2.11
+Version: 2.12a0
 Author: Enny van Beest, Celian Bimbard and Sam Dodgson
 Author-email: e.beest@ucl.ac.uk
 Requires-Python: >=3.7
@@ -11,12 +11,12 @@ License-File: LICENSE
 
 ## 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.
+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 *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.
+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 infomation Unit Match has calculated; for efficent usage of the GUI please look at *GUI_Reference_Guide.md* in the Demo Notebooks folder.
+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, this can be installed by `pip install mtscomp`.

{UnitMatchPy-2.11 → UnitMatchPy-2.12a0}/setup.py

@@ -5,7 +5,7 @@ with open('README.md', 'r') as f:
 
 setup(
     name="UnitMatchPy",
-    version="2.11",
+    version="2.12a",
     descriptin="Description of the package",
     author="Enny van Beest, Celian Bimbard and Sam Dodgson",
     author_email="e.beest@ucl.ac.uk",

UnitMatchPy-2.11/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
-```