IT-1137: enforce movie data type (#52)

* IT-1137 generalize author/email info

* IT-1137 ignore IDE config files

* IT-1137 fix movie data type inconsistency

* IT-1137 add missing maintainers info

* fixes for testing

---------

Co-authored-by: Nosheen Adil <[email protected]>

Author: brunoboivin

.gitignore

@@ -1,14 +1,11 @@
-# data
-
 # secrets
 .ideas-github-token
 
-
 # IDE
 *.sublime-workspace
 *.sublime-project
 .vscode/
-
+.idea/
 
 poetry.lock
 

Makefile

@@ -11,7 +11,17 @@ jupyter:
 install-poetry:
 	@bash install-poetry.sh
 
-test: 
+install: install-poetry
+	@echo "Installing py_isx..."
+	poetry check --lock || poetry lock
+	poetry install --verbose
+
+install-test: install-poetry
+	@echo "Installing py_isx & dependencies for testing..."
+	poetry check --lock || poetry lock
+	poetry install --extras "test" --verbose
+
+test: install-test
 	poetry run pytest -sx --failed-first
 
 test-pip:

install-poetry.sh

@@ -3,7 +3,5 @@ then
     echo "poetry could not be found, installing..."
     curl -sSL https://install.python-poetry.org | python3 -
     echo 'export PATH=$HOME/.local/bin:$PATH' >> ~/.bash_profile
-    # tell git to use SSH to get code
-    git config --global url.ssh://[email protected]/.insteadOf https://github.com/
     exit
 fi

isx/__init__.py

@@ -180,13 +180,10 @@ def get_frame_data(self, index: int):
 
         if self.footer["dataType"] == 0:
             bytes_per_pixel = 2
-            format_string = "H"
         elif self.footer["dataType"] == 1:
             bytes_per_pixel = 4
-            format_string = "f"
         elif self.footer["dataType"] == 2:
             bytes_per_pixel = 1
-            format_string = "b"
         else:
             raise NotImplementedError(
                 "Unknown number of bytes per pixel. Cannot decode this frame."
@@ -213,10 +210,8 @@ def get_frame_data(self, index: int):
 
         with open(self.file_path, mode="rb") as file:
             file.seek(index * n_bytes_per_frame)
-
             data = file.read(bytes_per_pixel * n_pixels)
-
-            frame = struct.unpack(format_string * n_pixels, data)
+            frame = np.frombuffer(data, dtype=self.data_type)
             frame = np.reshape(frame, self.spacing.num_pixels)
 
         return frame
@@ -374,11 +369,11 @@ def isxd_type(file_path: str) -> str:
     isx_datatype_mapping = {
         0: "miniscope_movie",
         1: "cell_set",
-        2: "isxd_behavioral_movie",  # not currently supported on IDEAS
+        2: "isxd_behavioral_movie",
         3: "gpio_data",
         4: "miniscope_image",
         5: "neural_events",
-        6: "isxd_metrics",  # not currently supported on IDEAS
+        6: "isxd_metrics",
         7: "imu_data",
         8: "vessel_set",
     }

mkdocs.yaml

@@ -1,5 +1,5 @@
 site_name: Python API for Inscopix Data
-site_author: Srinivas Gorur-Shandilya,  Zachary Ip
+site_author: Inscopix, Inc.
 repo_url: https://github.com/inscopix/py_isx
 repo_name: inscopix/py_isx
 site_url: https://inscopix.github.io/py_isx/

pyproject.toml

@@ -4,8 +4,8 @@
 name = "isx"
 version = "0.0.0.dev"
 description = "Python-based ISXD file reader"
-authors = ["Srinivas Gorur-Shandilya <[email protected]>", "Zachary Ip <Zachary.Ip@bruker.com>"]
-maintainers = ["Zachary Ip <Zachary.Ip@bruker.com>"]
+authors = ["Inscopix, Inc. <support@inscopix.com>"]
+maintainers = ["Inscopix, Inc. <support@inscopix.com>"]
 readme = "README.md"
 license = "CC-BY-NC-4.0"
 homepage = "https://github.com/inscopix/py_isx"

setup.py

@@ -31,10 +31,10 @@
     'version': '0.0.0.dev0',
     'description': 'Python-based ISXD file reader',
     'long_description': '# isx: pure-python API to read Inscopix data\n\n![](https://github.com/inscopix/py_isx/actions/workflows/main.yml/badge.svg) \n![](https://img.shields.io/pypi/v/isx)\n\nThis is a pure-python API to read Inscopix ISXD files. \n\n\n## Documentation\n\n[Read the documentation](https://inscopix.github.io/py_isx/)\n\n## Support\n\n|  File type | Support |\n|  --------- | ------- |\n| ISXD CellSet   | ✅ |\n| ISXD Movie   | ✅ |\n| ISXD Movie (multi-plane)   | ❌ |\n| ISXD Movie (dual-color)   | ❌ |\n| GPIO data   | ❌ |\n| ISXD Events   | ❌ |\n| ISXD VesselSet   | ❌ |\n\n\n## Install\n\n### Poetry\n\n```bash\npoetry add isx\n```\n\n### pip\n\n\n```bash\npip install isx\n```\n\n## Caution\n\nThis is a work in progress, and all reading functions in the IDPS Python API are not supported yet. \n\n\n## Testing\n\nThis code is tested using GitHub Actions on the following python\nversions:\n\n- 3.9\n- 3.10\n- 3.11\n- 3.12\n',
-    'author': 'Srinivas Gorur-Shandilya',
-    'author_email': 's.gorur_shandilya@bruker.com',
-    'maintainer': 'Zachary Ip',
-    'maintainer_email': 'Zachary.Ip@bruker.com',
+    'author': 'Inscopix, Inc.',
+    'author_email': 'support@inscopix.com',
+    'maintainer': 'Inscopix, Inc.',
+    'maintainer_email': 'support@inscopix.com',
     'url': 'https://github.com/inscopix/py_isx',
     'packages': packages,
     'package_data': package_data,

tests/test_isx.py

@@ -174,6 +174,8 @@ def test_movie_data_type(item):
         movie.data_type == item["dtype"]
     ), f"Could not correctly read data type of movie {movie_name}"
 
+    assert movie.data_type == movie.get_frame_data(0).dtype
+
 
 @pytest.mark.parametrize("item", movie_info)
 def test_movie_num_pixels(item):