From 08bb02baaf95a4eb3692fe4cc09fca299d073df7 Mon Sep 17 00:00:00 2001 From: rly Date: Wed, 3 Apr 2024 11:12:58 -0700 Subject: [PATCH 1/5] Fix issue importing scipy.special._cdflib in build --- nwb-guide.spec | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/nwb-guide.spec b/nwb-guide.spec index 67ba79cb4..eed83761b 100644 --- a/nwb-guide.spec +++ b/nwb-guide.spec @@ -12,7 +12,12 @@ from PyInstaller.utils.hooks import collect_all datas = [('./paths.config.json', '.'), ('./package.json', '.')] binaries = [] -hiddenimports = [ 'email_validator', *collect_submodules('scipy.special.cython_special'), *os.path.join(os.path.dirname(scipy.__file__), '.libs')] +hiddenimports = [ + 'email_validator', + *collect_submodules('scipy.special.cython_special'), + *collect_submodules('scipy.special._cdflib'), + *os.path.join(os.path.dirname(scipy.__file__), '.libs') +] datas += collect_data_files('jsonschema_specifications') tmp_ret = collect_all('dandi') From efb50525456e95f39482230f77824de58313713c Mon Sep 17 00:00:00 2001 From: Garrett Michael Flynn Date: Wed, 3 Apr 2024 11:24:15 -0700 Subject: [PATCH 2/5] Updates based on Ryan's feedback --- docs/tutorials/dataset.rst | 2 +- docs/tutorials/single_session.rst | 8 ++++---- pyflask/manageNeuroconv/manage_neuroconv.py | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/tutorials/dataset.rst b/docs/tutorials/dataset.rst index c0b2aca0a..6021a05ce 100644 --- a/docs/tutorials/dataset.rst +++ b/docs/tutorials/dataset.rst @@ -17,7 +17,7 @@ Navigate to the **Settings** page using the main sidebar. Then press the **Gener Press the Generate button on the Settings page to create the dataset. -The generated data will populate in the `~/NWB_GUIDE/test_data` directory and include a `data` folder with the original data as well as a `dataset` folder that duplicates this `data` across multiple subjects and sessions. +The generated data will populate in the ``~/NWB_GUIDE/test_data`` directory and include a `data` folder with the original data as well as a `dataset` folder that duplicates this `data` across multiple subjects and sessions. .. code-block:: bash diff --git a/docs/tutorials/single_session.rst b/docs/tutorials/single_session.rst index 6f1ba5744..3746ad8fa 100644 --- a/docs/tutorials/single_session.rst +++ b/docs/tutorials/single_session.rst @@ -3,7 +3,7 @@ Converting a Single Session As a researcher, you’ve just completed an experimental session and you’d like to convert your data to NWB right away. -Upon launching the GUIDE, you'll begin on the Conversions page. If you’re opening the application for the first time, there should be no pipelines listed on this page. +Upon launching the GUIDE, you'll begin on the Convert page. If you’re opening the application for the first time, there should be no pipelines listed on this page. .. figure:: ../assets/tutorials/home-page.png :align: center @@ -59,7 +59,7 @@ Next, you’ll specify the data formats you’re working with on the Data Format :align: center :alt: Date Formats page -The tutorial we're working with uses the SpikeGLX and Phy formats, a common output for NeuroPixel recordings and subsequent spike sorting. To specify that your pipeline will handle these files, you’ll press the “Add Format” button. +The tutorial we're working with uses the SpikeGLX and Phy formats, a common output for Neuropixels recordings and subsequent spike sorting. To specify that your pipeline will handle these files, you’ll press the “Add Format” button. .. figure:: ../assets/tutorials/single/format-options.png :align: center @@ -92,7 +92,7 @@ Source Data Information ^^^^^^^^^^^^^^^^^^^^^^^ On this page, specify the relevant **.bin** (Spikeglx) file and **phy** folder so that the GUIDE can find this source data to complete the conversion. -As discussed in the :doc:`Dataset Generation ` tutorial, these can be found in the `~/NWB_GUIDE/test-data/data` directory. +As discussed in the :doc:`Dataset Generation ` tutorial, these can be found in the ``~/NWB_GUIDE/test-data/data`` directory. You can either click the file selector to navigate to the file or drag-and-drop into the GUIDE from your file navigator. @@ -112,7 +112,7 @@ The Session Start Time in the General Metadata section is already specified beca :alt: Metadata page with invalid Subject information -However, we still need to add the Subject information—as noted by the red accents around that item. Let’s say that our subject is a male mouse with an age of P30D. +However, we still need to add the Subject information—as noted by the red accents around that item. Let’s say that our subject is a male mouse with an age of P30D, which represents 30 days old. .. figure:: ../assets/tutorials/single/metadata-subject-complete.png :align: center diff --git a/pyflask/manageNeuroconv/manage_neuroconv.py b/pyflask/manageNeuroconv/manage_neuroconv.py index 500382e4c..9f6fb3e94 100644 --- a/pyflask/manageNeuroconv/manage_neuroconv.py +++ b/pyflask/manageNeuroconv/manage_neuroconv.py @@ -1062,7 +1062,7 @@ def generate_test_data(output_path: str): spikeglx_output_folder = base_path / "spikeglx" phy_output_folder = base_path / "phy" - # Define NeuroPixel-like values for sampling rates and conversion factors + # Define Neuropixels-like values for sampling rates and conversion factors duration_in_s = 3.0 number_of_units = 50 number_of_channels = 385 # Have to include 'sync' channel to be proper SpikeGLX. TODO: artificiate sync pulses From 7ba2faf99ae33c8c4e5260795fb964ea398dd8d7 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Wed, 3 Apr 2024 14:30:01 -0400 Subject: [PATCH 3/5] Update docs/tutorials/dataset.rst Co-authored-by: Ryan Ly --- docs/tutorials/dataset.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tutorials/dataset.rst b/docs/tutorials/dataset.rst index 6021a05ce..0995f918d 100644 --- a/docs/tutorials/dataset.rst +++ b/docs/tutorials/dataset.rst @@ -17,7 +17,7 @@ Navigate to the **Settings** page using the main sidebar. Then press the **Gener Press the Generate button on the Settings page to create the dataset. -The generated data will populate in the ``~/NWB_GUIDE/test_data`` directory and include a `data` folder with the original data as well as a `dataset` folder that duplicates this `data` across multiple subjects and sessions. +The generated data will populate in the ``~/NWB_GUIDE/test_data`` directory and include a ``data`` folder with the original data as well as a ``dataset`` folder that duplicates this ``data`` across multiple subjects and sessions. .. code-block:: bash From 0033ac6cd3a0843276001bd9fa76677c4831e96a Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Wed, 3 Apr 2024 14:32:50 -0400 Subject: [PATCH 4/5] try removing pin --- environments/environment-Windows.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/environments/environment-Windows.yml b/environments/environment-Windows.yml index 4066ffefd..fc1e15850 100644 --- a/environments/environment-Windows.yml +++ b/environments/environment-Windows.yml @@ -22,4 +22,3 @@ dependencies: - pytest == 7.2.2 - pytest-cov == 4.1.0 - scikit-learn == 1.4.0 - - scipy == 1.12.0 From 1906396f06c6f1662d03c54d6f403cc0080c8ee0 Mon Sep 17 00:00:00 2001 From: Garrett Michael Flynn Date: Wed, 3 Apr 2024 11:40:43 -0700 Subject: [PATCH 5/5] Remove output location node and add to next steps --- docs/tutorials/next_steps.rst | 12 +++++++++++- docs/tutorials/single_session.rst | 7 ------- 2 files changed, 11 insertions(+), 8 deletions(-) diff --git a/docs/tutorials/next_steps.rst b/docs/tutorials/next_steps.rst index ce80155c6..daf330370 100644 --- a/docs/tutorials/next_steps.rst +++ b/docs/tutorials/next_steps.rst @@ -1,3 +1,13 @@ What's Next? ======================================= -Coming soon... + +Considerations when Using Your Own Data +--------------------------------------- +When using your own data, there are a few things to consider: + +Choosing an Output Location +^^^^^^^^^^^^^^^^^^^^^^^^^^^ + Choosing a good output location is important for two reasons, namely **conversion speed** and **disk space**. + + 1. SSDs will be much faster than HDDs. We’d recommend moving the output location to an SSD if available. + 2. If you don’t have much disk space available on your main drive, we recommend changing the output location to a drive that has ample space. diff --git a/docs/tutorials/single_session.rst b/docs/tutorials/single_session.rst index 3746ad8fa..6eabe32d9 100644 --- a/docs/tutorials/single_session.rst +++ b/docs/tutorials/single_session.rst @@ -19,13 +19,6 @@ Project Setup The Project Setup page will have you define two pieces of information about your pipeline: the **name** and, optionally, the **output location** for your NWB files. -.. note:: - Choosing a good output location is important for two reasons, namely **conversion speed** and **disk space**. - - 1. SSDs will be much faster than HDDs. We’d recommend moving the output location to an SSD if available. - 2. If you don’t have much disk space available on your main drive, we recommend changing the output location to a drive that has ample space. - - You’ll notice that the name property has a red asterisk next to it, which identifies it as a required property. .. figure:: ../assets/tutorials/single/info-page.png