actinet 0.0.dev4__tar.gz → 0.0.dev6__tar.gz

{actinet-0.0.dev4 → actinet-0.0.dev6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: actinet
-Version: 0.0.dev4
+Version: 0.0.dev6
 Summary: Activity detection algorithm compatible with the UK Biobank Accelerometer Dataset
 Home-page: https://github.com/OxWearables/actinet
 Download-URL: https://github.com/OxWearables/actinet
@@ -60,16 +60,16 @@ You are all set! The next time that you want to use `actinet`, open the Anaconda
 
 ```bash
 # Process an AX3 file
-$ actinet sample.cwa
+$ actinet -f sample.cwa
 
 # Or an ActiGraph file
-$ actinet sample.gt3x
+$ actinet -f sample.gt3x
 
 # Or a GENEActiv file
-$ actinet sample.bin
+$ actinet -f sample.bin
 
 # Or a CSV file (see data format below)
-$ actinet sample.csv
+$ actinet -f sample.csv
 ```
 
 ### Troubleshooting
@@ -77,7 +77,29 @@ $ actinet sample.csv
 Some systems may face issues with Java when running the script. If this is your case, try fixing OpenJDK to version 8:
 
 ```console
-conda install -n actinet openjdk=8
+conda create -n actinet openjdk=8
+```
+
+### Offline usage
+
+To use this package offline, one must first download and install the relevant classifier file and model modules.
+This repository offers two ways of doing this.
+
+Run the following code when you have internet access:
+```console
+actinet --cache-classifier
+```
+ 
+Following this, the actinet classifier can be used as standard without internet access, without needing to specify the flags relating to the model repository.
+ 
+Alternatively, you can download or git clone the ssl modules from the [ssl-wearables repository](https://github.com/OxWearables/ssl-wearables).
+
+In addition, you can donwload/prepare a custom classifier file.
+
+Once this is downloaded to an appopriate location, you can run the actinet model using:
+ 
+```console
+actinet -f sample.cwa -c /path/to/classifier.joblib.lzma -m /path/to/ssl-wearables
 ```
 
 ### Output files
@@ -85,7 +107,7 @@ conda install -n actinet openjdk=8
 By default, output files will be stored in a folder named after the input file, `outputs/{filename}/`, created in the current working directory. You can change the output path with the `-o` flag:
 
 ```console
-$ actinet sample.cwa -o /path/to/some/folder/
+$ actinet -f sample.cwa -o /path/to/some/folder/
 
 <Output summary written to: /path/to/some/folder/sample-outputSummary.json>
 <Time series output written to: /path/to/some/folder/sample-timeSeries.csv.gz>
@@ -103,7 +125,7 @@ See [Data Dictionary](https://biobankaccanalysis.readthedocs.io/en/latest/datadi
 To plot the activity profiles, you can use the -p flag:
 
 ```console
-$ actinet sample.cwa -p
+$ actinet -f sample.cwa -p
 <Output plot written to: data/sample-timeSeries-plot.png>
 ```
 
@@ -138,9 +160,9 @@ To process multiple files you can create a text file in Notepad which includes o
 Example text file *commands.txt*:
 
 ```console
-actinet file1.cwa &
-actinet file2.cwa &
-actinet file3.cwa 
+actinet -f file1.cwa &
+actinet -f file2.cwa &
+actinet -f file3.cwa 
 :END
 ````
 
@@ -151,9 +173,9 @@ Once this file is created, run `cmd < commands.txt` from the terminal.
 Create a file *command.sh* with:
 
 ```console
-actinet file1.cwa
-actinet file2.cwa
-actinet file3.cwa
+actinet -f file1.cwa
+actinet -f file2.cwa
+actinet -f file3.cwa
 ```
 
 Then, run `bash command.sh` from the terminal.

{actinet-0.0.dev4 → actinet-0.0.dev6}/README.md

@@ -38,16 +38,16 @@ You are all set! The next time that you want to use `actinet`, open the Anaconda
 
 ```bash
 # Process an AX3 file
-$ actinet sample.cwa
+$ actinet -f sample.cwa
 
 # Or an ActiGraph file
-$ actinet sample.gt3x
+$ actinet -f sample.gt3x
 
 # Or a GENEActiv file
-$ actinet sample.bin
+$ actinet -f sample.bin
 
 # Or a CSV file (see data format below)
-$ actinet sample.csv
+$ actinet -f sample.csv
 ```
 
 ### Troubleshooting
@@ -55,7 +55,29 @@ $ actinet sample.csv
 Some systems may face issues with Java when running the script. If this is your case, try fixing OpenJDK to version 8:
 
 ```console
-conda install -n actinet openjdk=8
+conda create -n actinet openjdk=8
+```
+
+### Offline usage
+
+To use this package offline, one must first download and install the relevant classifier file and model modules.
+This repository offers two ways of doing this.
+
+Run the following code when you have internet access:
+```console
+actinet --cache-classifier
+```
+ 
+Following this, the actinet classifier can be used as standard without internet access, without needing to specify the flags relating to the model repository.
+ 
+Alternatively, you can download or git clone the ssl modules from the [ssl-wearables repository](https://github.com/OxWearables/ssl-wearables).
+
+In addition, you can donwload/prepare a custom classifier file.
+
+Once this is downloaded to an appopriate location, you can run the actinet model using:
+ 
+```console
+actinet -f sample.cwa -c /path/to/classifier.joblib.lzma -m /path/to/ssl-wearables
 ```
 
 ### Output files
@@ -63,7 +85,7 @@ conda install -n actinet openjdk=8
 By default, output files will be stored in a folder named after the input file, `outputs/{filename}/`, created in the current working directory. You can change the output path with the `-o` flag:
 
 ```console
-$ actinet sample.cwa -o /path/to/some/folder/
+$ actinet -f sample.cwa -o /path/to/some/folder/
 
 <Output summary written to: /path/to/some/folder/sample-outputSummary.json>
 <Time series output written to: /path/to/some/folder/sample-timeSeries.csv.gz>
@@ -81,7 +103,7 @@ See [Data Dictionary](https://biobankaccanalysis.readthedocs.io/en/latest/datadi
 To plot the activity profiles, you can use the -p flag:
 
 ```console
-$ actinet sample.cwa -p
+$ actinet -f sample.cwa -p
 <Output plot written to: data/sample-timeSeries-plot.png>
 ```
 
@@ -116,9 +138,9 @@ To process multiple files you can create a text file in Notepad which includes o
 Example text file *commands.txt*:
 
 ```console
-actinet file1.cwa &
-actinet file2.cwa &
-actinet file3.cwa 
+actinet -f file1.cwa &
+actinet -f file2.cwa &
+actinet -f file3.cwa 
 :END
 ````
 
@@ -129,9 +151,9 @@ Once this file is created, run `cmd < commands.txt` from the terminal.
 Create a file *command.sh* with:
 
 ```console
-actinet file1.cwa
-actinet file2.cwa
-actinet file3.cwa
+actinet -f file1.cwa
+actinet -f file2.cwa
+actinet -f file3.cwa
 ```
 
 Then, run `bash command.sh` from the terminal.

{actinet-0.0.dev4 → actinet-0.0.dev6}/src/actinet/__init__.py

@@ -4,8 +4,8 @@ __maintainer__ = "Shing Chan"
 __maintainer_email__ = "shing.chan@ndph.ox.ac.uk"
 __license__ = "See LICENSE file."
 
-__model_version__ = "ssl_ukb_c24_rw_20240204"
-__model_md5__ = "84f3d5bb73de5c4da057918c45400da4"
+__classifier_version__ = "ssl_ukb_c24_rw_20240204"
+__classifier_md5__ = "11c3f36348dae37da4f99bd6d810bbb2"
 
 from . import _version
 

{actinet-0.0.dev4 → actinet-0.0.dev6}/src/actinet/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-02-05T14:38:16+0000",
+ "date": "2024-03-09T08:28:09+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "5857a41418deef2d09568018e05ecae250c54d14",
- "version": "0.0.dev4"
+ "full-revisionid": "5b419d5fe6079975dbc6ccbca13b128c52709f3f",
+ "version": "0.0.dev6"
 }
 '''  # END VERSION_JSON
 

{actinet-0.0.dev4 → actinet-0.0.dev6}/src/actinet/actinet.py

@@ -12,15 +12,14 @@ import joblib
 
 import actipy
 
-from actinet import __model_version__
-from actinet import __model_md5__
+from actinet import __classifier_version__
+from actinet import __classifier_md5__
 from actinet.accPlot import plotTimeSeries
 from actinet.models import ActivityClassifier
-from actinet.sslmodel import SAMPLE_RATE
-from actinet.summarisation import getActivitySummary, ACTIVITY_LABELS
+from actinet.summarisation import getActivitySummary
 from actinet.utils.utils import infer_freq
 
-BASE_URL = "https://zenodo.org/records/10619096/files/"
+BASE_URL = "https://zenodo.org/records/10625542/files/"
 
 
 def main():
@@ -37,10 +36,15 @@ def main():
         default="outputs/",
     )
     parser.add_argument(
-        "--model-path", "-m", help="Enter custom model file to use", default=None
+        "--classifier-path",
+        "-c",
+        help="Enter custom acitivty classifier file to use",
+        default=None,
     )
     parser.add_argument(
-        "--force-download", action="store_true", help="Force download of model file"
+        "--force-download",
+        action="store_true",
+        help="Force download of classifier file",
     )
     parser.add_argument(
         "--pytorch-device",
@@ -63,12 +67,12 @@ def main():
         help="Plot the predicted activity labels",
     )
     parser.add_argument(
-        "--cache-ssl",
+        "--cache-classifier",
         action="store_true",
-        help="Download and cache ssl module for offline usage",
+        help="Download and cache classifier file and model modules for offline usage",
     )
     parser.add_argument(
-        "--ssl-repo-path", "-s", help="Enter repository of ssl model", default=None
+        "--model-repo-path", "-m", help="Enter repository of ssl model", default=None
     )
     parser.add_argument("--quiet", "-q", action="store_true", help="Suppress output")
     args = parser.parse_args()
@@ -77,18 +81,32 @@ def main():
 
     verbose = not args.quiet
 
-    if args.cache_ssl:
-        model = ActivityClassifier(weights_path=None, ssl_repo=None, verbose=verbose, labels=ACTIVITY_LABELS)
+    classifier_path = (
+        pathlib.Path(__file__).parent / f"{__classifier_version__}.joblib.lzma"
+    )
+
+    if args.cache_classifier:
+        load_classifier(
+            classifier_path=classifier_path,
+            model_repo_path=None,
+            check_md5=True,
+            force_download=True,
+            verbose=verbose,
+        )
 
         after = time.time()
         print(f"Done! ({round(after - before,2)}s)")
 
         return
 
+    else:
+        if not args.filepath:
+            raise ValueError("Please provide a file to process.")
+
     # Load file
     data, info = read(
         args.filepath,
-        resample_hz=SAMPLE_RATE,
+        resample_hz=None,
         sample_rate=args.sample_rate,
         verbose=verbose,
     )
@@ -98,21 +116,25 @@ def main():
     outdir = os.path.join(args.outdir, basename)
     os.makedirs(outdir, exist_ok=True)
 
-    # Run model
+    # Run classifier
     if verbose:
-        print("Loading model...")
-    model_path = pathlib.Path(__file__).parent / f"{__model_version__}.joblib.lzma"
-    check_md5 = args.model_path is None
-    model: ActivityClassifier = load_model(
-        args.model_path or model_path, check_md5, args.force_download, verbose
+        print("Loading classifier...")
+
+    check_md5 = args.classifier_path is None
+    classifier: ActivityClassifier = load_classifier(
+        args.classifier_path or classifier_path,
+        args.model_repo_path,
+        check_md5,
+        args.force_download,
+        verbose,
     )
 
-    model.verbose = verbose
-    model.device = args.pytorch_device
+    classifier.verbose = verbose
+    classifier.device = args.pytorch_device
 
     if verbose:
         print("Running activity classifier...")
-    Y = model.predict_from_frame(data)
+    Y = classifier.predict_from_frame(data, args.sample_rate)
 
     # Save predicted activities
     timeSeriesFile = f"{outdir}/{basename}-timeSeries.csv.gz"
@@ -121,8 +143,17 @@ def main():
     if verbose:
         print("Time series output written to:", timeSeriesFile)
 
+    # Plot activity profile
+    if args.plot_activity:
+        plotFile = f"{outdir}/{basename}-timeSeries-plot.png"
+        fig = plotTimeSeries(Y)
+        fig.savefig(plotFile, dpi=200, bbox_inches="tight")
+
+        if verbose:
+            print("Output plot written to:", plotFile)
+
     # Summary
-    summary = getActivitySummary(Y, True, True, verbose)
+    summary = getActivitySummary(Y, list(classifier.labels), True, True, verbose)
 
     # Join the actipy processing info, with acitivity summary data
     outputSummary = {**summary, **info}
@@ -139,34 +170,33 @@ def main():
     if verbose:
         print("\nSummary Stats\n---------------------")
         print(
-            {
-                key: outputSummary[key]
-                for key in [
-                    "Filename",
-                    "Filesize(MB)",
-                    "WearTime(days)",
-                    "NonwearTime(days)",
-                    "ReadOK",
-                    "acc-overall-avg(mg)",
-                ]
-                + [f"{label}-week-avg" for label in ACTIVITY_LABELS]
-            }
+            json.dumps(
+                {
+                    key: outputSummary[key]
+                    for key in [
+                        "Filename",
+                        "Filesize(MB)",
+                        "WearTime(days)",
+                        "NonwearTime(days)",
+                        "ReadOK",
+                    ]
+                    + [
+                        f"{label}-overall-avg"
+                        for label in ["acc"] + list(classifier.labels)
+                    ]
+                },
+                indent=4,
+                cls=NpEncoder,
+            )
         )
 
-    # Plot activity profile
-    if args.plot_activity:
-        plotFile = f"{outdir}/{basename}-timeSeries-plot.png"
-        fig = plotTimeSeries(Y)
-        fig.savefig(plotFile, dpi=200, bbox_inches="tight")
-
-        if verbose:
-            print("Output plot written to:", plotFile)
-
     after = time.time()
     print(f"Done! ({round(after - before,2)}s)")
 
 
-def read(filepath, resample_hz="uniform", sample_rate=None, verbose=True):
+def read(
+    filepath, resample_hz="uniform", sample_rate=None, lowpass_hz=None, verbose=True
+):
 
     p = pathlib.Path(filepath)
     ftype = p.suffixes[0].lower()
@@ -197,7 +227,7 @@ def read(filepath, resample_hz="uniform", sample_rate=None, verbose=True):
         data, info = actipy.process(
             data,
             sample_rate,
-            lowpass_hz=None,
+            lowpass_hz=lowpass_hz,
             calibrate_gravity=True,
             detect_nonwear=True,
             resample_hz=resample_hz,
@@ -218,7 +248,7 @@ def read(filepath, resample_hz="uniform", sample_rate=None, verbose=True):
 
         data, info = actipy.read_device(
             filepath,
-            lowpass_hz=None,
+            lowpass_hz=lowpass_hz,
             calibrate_gravity=True,
             detect_nonwear=True,
             resample_hz=resample_hz,
@@ -240,14 +270,20 @@ def resolve_path(path):
     return dirname, filename, extension
 
 
-def load_model(model_path, ssl_repo_path=None, check_md5=True, force_download=False, verbose=True):
-    """Load trained model. Download if not exists."""
+def load_classifier(
+    classifier_path,
+    model_repo_path=None,
+    check_md5=True,
+    force_download=False,
+    verbose=True,
+):
+    """Load trained classifier. Download if not exists."""
 
-    pth = pathlib.Path(model_path)
+    pth = pathlib.Path(classifier_path)
 
     if force_download or not pth.exists():
 
-        url = f"{BASE_URL}{__model_version__}.joblib.lzma"
+        url = f"{BASE_URL}{__classifier_version__}.joblib.lzma"
 
         if verbose:
             print(f"Downloading {url}...")
@@ -256,20 +292,19 @@ def load_model(model_path, ssl_repo_path=None, check_md5=True, force_download=Fa
             shutil.copyfileobj(f_src, f_dst)
 
     if check_md5:
-        assert md5(pth) == __model_md5__, (
-            "Model file is corrupted. Please run with --force-download "
+        assert md5(pth) == __classifier_md5__, (
+            "Classifier file is corrupted. Please run with --force-download "
             "to download the model file again."
         )
 
-    model: ActivityClassifier = joblib.load(pth)
+    classifier: ActivityClassifier = joblib.load(pth)
 
-    if ssl_repo_path and pathlib.Path(ssl_repo_path).exists():
-        if verbose:
-            print(f"Loading ssl repository from {ssl_repo_path}.")
+    if model_repo_path and pathlib.Path(model_repo_path).exists() and verbose:
+        print(f"Loading model repository from {model_repo_path}.")
 
-        model = model.load_ssl(ssl_repo_path)
+    classifier.load_model(model_repo_path)
 
-    return model
+    return classifier
 
 
 def md5(fname):