Merge branch 'main' of https://github.com/datajoint/element-interface

Author: kushalbakshi

.gitignore

@@ -114,4 +114,3 @@ dj_local_conf_old.json
 **/*~
 **/#*#
 **/.#*
-docker-compose.y*ml

CHANGELOG.md

@@ -2,14 +2,11 @@
 
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
-## [0.3.2] - 2022-12-14
-
-+ Update - PrairieView metadata includes recording start time
-
-## [0.3.1] - Unreleased
+## [0.4.0] - 2022-12-14
 
 + Add - mkdocs documentation
 + Add - improved docstrings for mkdocs
++ Add - EXTRACT trigger and loader tools
 
 ## [0.3.0] - 2022-10-7
 
@@ -40,6 +37,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 
 + Add - Readers for: `ScanImage`, `Suite2p`, `CaImAn`.
 
+[0.4.0]: https://github.com/datajoint/element-interface/releases/tag/0.4.0
 [0.3.0]: https://github.com/datajoint/element-interface/releases/tag/0.3.0
 [0.2.1]: https://github.com/datajoint/element-interface/releases/tag/0.2.1
 [0.2.0]: https://github.com/datajoint/element-interface/releases/tag/0.2.0

docs/docker-compose.yaml

@@ -0,0 +1,51 @@
+# MODE="LIVE|QA|PUSH" PACKAGE=element_interface UPSTREAM_REPO=https://github.com/datajoint/element-interface.git HOST_UID=$(id -u) docker compose -f docs/docker-compose.yaml up --build
+#
+# navigate to http://localhost/
+version: "2.4"
+services:
+  docs:
+    build:
+      dockerfile: docs/.docker/Dockerfile
+      context: ../
+      args:
+        - PACKAGE
+    image: ${PACKAGE}-docs
+    environment:
+      - PACKAGE
+      - UPSTREAM_REPO
+      - MODE
+      - GOOGLE_ANALYTICS_KEY 
+      - PATCH_VERSION
+    volumes:
+      - ../docs:/main/docs
+      - ../${PACKAGE}:/main/${PACKAGE}
+    user: ${HOST_UID}:anaconda
+    ports:
+      - 80:80
+    command:
+      - sh
+      - -c
+      - |
+        git config --global --add safe.directory /main
+        set -e
+        export PATCH_VERSION=$$(cat /main/$${PACKAGE}/version.py | grep -oE '\d+\.\d+\.[a-z0-9]+')
+        if echo "$${MODE}" | grep -i live &>/dev/null; then
+            mkdocs serve --config-file ./docs/mkdocs.yaml -a 0.0.0.0:80
+        elif echo "$${MODE}" | grep -iE "qa|push" &>/dev/null; then
+            echo "INFO::Delete gh-pages branch"
+            git branch -D gh-pages || true
+            echo "INFO::Fetch upstream gh-pages"
+            git fetch $${UPSTREAM_REPO} gh-pages:gh-pages && git switch gh-pages || git switch --orphan gh-pages && git commit --allow-empty -m "init commit"
+            echo "INFO::mike"
+            mike deploy --config-file ./docs/mkdocs.yaml -u $$(grep -oE '\d+\.\d+' /main/$${PACKAGE}/version.py) latest
+            mike set-default --config-file ./docs/mkdocs.yaml latest
+            if echo "$${MODE}" | grep -i qa &>/dev/null; then
+                mike serve --config-file ./docs/mkdocs.yaml -a 0.0.0.0:80
+            elif echo "$${MODE}" | grep -i push &>/dev/null; then
+                echo "INFO::Push gh-pages to upstream"
+                git push $${UPSTREAM_REPO} gh-pages
+            fi
+        else
+            echo "Unexpected mode..."
+            exit 1
+        fi

element_interface/extract_loader.py

@@ -0,0 +1,59 @@
+import os
+import numpy as np
+from pathlib import Path
+from datetime import datetime
+
+
+class EXTRACT_loader:
+    def __init__(self, extract_dir: str):
+        """Initialize EXTRACT loader class
+
+        Args:
+            extract_dir (str): string, absolute file path to EXTRACT directory
+
+        Raises:
+            FileNotFoundError: Could not find EXTRACT results
+        """
+        from scipy.io import loadmat
+
+        try:
+            extract_file = next(Path(extract_dir).glob("*_extract_output.mat"))
+        except StopInteration:
+            raise FileNotFoundError(
+                f"EXTRACT output result file is not found at {extract_dir}."
+            )
+
+        results = loadmat(extract_file)
+
+        self.creation_time = datetime.fromtimestamp(os.stat(extract_file).st_ctime)
+        self.S = results["output"][0]["spatial_weights"][0]  # (Height, Width, MaskId)
+        self.T = results["output"][0]["temporal_weights"][0]  # (Time, MaskId)
+
+    def load_results(self):
+        """Load the EXTRACT results
+        
+        Returns:
+            masks (dict): Details of the masks identified with the EXTRACT segmentation package.
+        """
+        from scipy.sparse import find
+
+        S_transposed = self.S.transpose([2, 0, 1])  # MaskId, Height, Width
+
+        masks = []
+
+        for mask_id, s in enumerate(S_transposed):
+            ypixels, xpixels, weights = find(s)
+            masks.append(
+                dict(
+                    mask_id=mask_id,
+                    mask_npix=len(weights),
+                    mask_weights=weights,
+                    mask_center_x=int(np.average(xpixels, weights=weights) + 0.5),
+                    mask_center_y=int(np.average(ypixels, weights=weights) + 0.5),
+                    mask_center_z=None,
+                    mask_xpix=xpixels,
+                    mask_ypix=ypixels,
+                    mask_zpix=None,
+                )
+            )
+        return masks

element_interface/extract_trigger.py

@@ -0,0 +1,91 @@
+import os
+from typing import Union
+from pathlib import Path
+from textwrap import dedent
+from datetime import datetime
+
+
+class EXTRACT_trigger:
+    m_template = dedent(
+        """
+        % Load Data
+        data = load('{scanfile}');
+        M = data.M;
+        
+        % Input Paramaters
+        config = struct();
+        {parameters_list_string}
+        
+        % Run EXTRACT
+        output = extractor(M, config);
+        save('{output_fullpath}', 'output');
+        """
+    )
+
+    def __init__(
+        self,
+        scanfile: Union[str, Path],
+        parameters: dict,
+        output_dir: Union[str, Path],
+    ) -> None:
+        """A helper class to trigger EXTRACT analysis in element-calcium-imaging.
+
+        Args:
+            scanfile (Union[str, Path]): Full path of the scan
+            parameters (dict): EXTRACT input paramaters.
+            output_dir (Union[str, Path]): Directory to store the outputs of EXTRACT analysis.
+        """
+        assert isinstance(parameters, dict)
+
+        self.scanfile = Path(scanfile)
+        self.output_dir = Path(output_dir)
+        self.parameters = parameters
+
+    def write_matlab_run_script(self):
+        """Compose a matlab script and save it with the name run_extract.m.
+
+        The composed script is basically the formatted version of the m_template attribute."""
+
+        self.output_fullpath = (
+            self.output_dir / f"{self.scanfile.stem}_extract_output.mat"
+        )
+
+        m_file_content = self.m_template.format(
+            **dict(
+                parameters_list_string="\n".join(
+                    [
+                        f"config.{k} = '{v}';"
+                        if isinstance(v, str)
+                        else f"config.{k} = {str(v).lower()};"
+                        if isinstance(v, bool)
+                        else f"config.{k} = {v};"
+                        for k, v in self.parameters.items()
+                    ]
+                ),
+                scanfile=self.scanfile.as_posix(),
+                output_fullpath=self.output_fullpath.as_posix(),
+            )
+        ).lstrip()
+
+        self.m_file_fp = self.output_dir / "run_extract.m"
+
+        with open(self.m_file_fp, "w") as f:
+            f.write(m_file_content)
+
+    def run(self):
+        """Run the matlab run_extract.m script."""
+
+        self.write_matlab_run_script()
+
+        current_dir = Path.cwd()
+        os.chdir(self.output_dir)
+
+        try:
+            import matlab.engine
+
+            eng = matlab.engine.start_matlab()
+            eng.run_extract()
+        except Exception as e:
+            raise e
+        finally:
+            os.chdir(current_dir)

element_interface/version.py

@@ -1,3 +1,3 @@
 """Package metadata"""
 
-__version__ = "0.3.2"
+__version__ = "0.4.0"