viewephys 1.2.0__tar.gz → 1.3.0__tar.gz

{viewephys-1.2.0 → viewephys-1.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: viewephys
-Version: 1.2.0
+Version: 1.3.0
 Summary: Neuropixel raw data viewer
 Author: Olivier Winter
 License: MIT
@@ -18,6 +18,10 @@ Requires-Dist: pandas
 Requires-Dist: pyqtgraph>=0.13.1
 Requires-Dist: qtpy
 Requires-Dist: scipy
+Requires-Dist: spikeinterface
+Provides-Extra: lfpack
+Requires-Dist: lfpack; extra == "lfpack"
+Requires-Dist: iblatlas; extra == "lfpack"
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: pytest-qt; extra == "dev"
@@ -77,7 +81,7 @@ When the picking mode is enabled (menu pick)
 
 ## Examples
 
-### Visualize raw binary file
+### Visualize raw binary file through the command line
 Activate your environment and type `viewephys`, you can then load a neuropixel binary file using the file menu.
 
 ![alt text](./docs/raw_bin_viewer_destripe.png "Ephys viewer ")
@@ -88,6 +92,11 @@ viewphys -f /path/to/raw.bin
 ```
 
 ### Load in a numpy array or slice
+
+`viewephys` can be used through the Python console or iPython, allowing you to create
+multiple instances of the viewer at once.
+
+
 ```python
 # if running ipython, you may have to use the `%gui qt` magic command
 import numpy as np
@@ -95,10 +104,49 @@ from viewephys.gui import viewephys
 nc, ns, fs = (384, 50000, 30000)  # this mimics one second of neuropixel data
 data = np.random.randn(nc, ns) / 1e6  # volts by default
 ve = viewephys(data, fs=fs)
+
+# We can open multiple windows at once, but they must have different titles
+data2 = data * 50
+ve2 = viewephys(data, fs=fs, title="plot 2")
+
 ```
 ![alt text](./docs/view_rand_array.png "Ephys viewer")
 
 
+Note if you are running through a script, you need to instantiate
+the Qt application yourself:
+
+#### Opening a binary file through a script
+
+```python
+from viewephys.gui import EphysBinViewer, create_app
+
+app = create_app()
+
+viewer = EphysBinViewer(r"C:\Users\Joe\Desktop\1119617_LSE1_shank12_g0_imec0\1119617_LSE1_shank12_g0_t0.imec0.ap.bin")
+
+app.exec()
+```
+
+#### Load in a numpy array or slice through a script
+
+```python
+
+import numpy as np
+from viewephys.gui import viewephys, create_app
+
+app = create_app()
+
+nc, ns, fs = (384, 50000, 30000)  # this mimics one second of neuropixel data
+data = np.random.randn(nc, ns) / 1e6  # volts by default
+
+ve = viewephys(data, fs=fs)
+ve2 = viewephys(data * 50, fs=fs, title="plot 2")
+
+app.exec()
+
+```
+
 ## Contribution
 Fork and PR.
 

{viewephys-1.2.0 → viewephys-1.3.0}/README.md

@@ -36,7 +36,7 @@ When the picking mode is enabled (menu pick)
 
 ## Examples
 
-### Visualize raw binary file
+### Visualize raw binary file through the command line
 Activate your environment and type `viewephys`, you can then load a neuropixel binary file using the file menu.
 
 ![alt text](./docs/raw_bin_viewer_destripe.png "Ephys viewer ")
@@ -47,6 +47,11 @@ viewphys -f /path/to/raw.bin
 ```
 
 ### Load in a numpy array or slice
+
+`viewephys` can be used through the Python console or iPython, allowing you to create
+multiple instances of the viewer at once.
+
+
 ```python
 # if running ipython, you may have to use the `%gui qt` magic command
 import numpy as np
@@ -54,10 +59,49 @@ from viewephys.gui import viewephys
 nc, ns, fs = (384, 50000, 30000)  # this mimics one second of neuropixel data
 data = np.random.randn(nc, ns) / 1e6  # volts by default
 ve = viewephys(data, fs=fs)
+
+# We can open multiple windows at once, but they must have different titles
+data2 = data * 50
+ve2 = viewephys(data, fs=fs, title="plot 2")
+
 ```
 ![alt text](./docs/view_rand_array.png "Ephys viewer")
 
 
+Note if you are running through a script, you need to instantiate
+the Qt application yourself:
+
+#### Opening a binary file through a script
+
+```python
+from viewephys.gui import EphysBinViewer, create_app
+
+app = create_app()
+
+viewer = EphysBinViewer(r"C:\Users\Joe\Desktop\1119617_LSE1_shank12_g0_imec0\1119617_LSE1_shank12_g0_t0.imec0.ap.bin")
+
+app.exec()
+```
+
+#### Load in a numpy array or slice through a script
+
+```python
+
+import numpy as np
+from viewephys.gui import viewephys, create_app
+
+app = create_app()
+
+nc, ns, fs = (384, 50000, 30000)  # this mimics one second of neuropixel data
+data = np.random.randn(nc, ns) / 1e6  # volts by default
+
+ve = viewephys(data, fs=fs)
+ve2 = viewephys(data * 50, fs=fs, title="plot 2")
+
+app.exec()
+
+```
+
 ## Contribution
 Fork and PR.
 

{viewephys-1.2.0 → viewephys-1.3.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "viewephys"
-version = "1.2.0"
+version = "1.3.0"
 description = "Neuropixel raw data viewer"
 authors = [
     { name = "Olivier Winter" },
@@ -20,6 +20,7 @@ dependencies = [
     "pyqtgraph>=0.13.1",
     "qtpy",
     "scipy",
+    "spikeinterface",
 ]
 
 [project.readme]
@@ -30,6 +31,10 @@ content-type = "text/markdown"
 text = "MIT"
 
 [project.optional-dependencies]
+lfpack = [
+    "lfpack",
+    "iblatlas",
+]
 dev = [
     "pytest",
     "pytest-qt",

{viewephys-1.2.0 → viewephys-1.3.0}/src/viewephys/command_line.py

@@ -24,16 +24,29 @@ def viewephys():
         "-f",
         "--file",
         default=None,
-        help="path to the binary file to load",
+        help="path to the binary or lfpack .h5 file to load",
         required=False,
     )
+    parser.add_argument(
+        "--lfpack",
+        action="store_true",
+        help="open the lfpack HDF5 viewer (auto-selected for .h5/.hdf5 files)",
+    )
     args = parser.parse_args()  # returns data from the options specified (echo)
     print(args.file)
-    from viewephys.gui import EphysBinViewer
+    from pathlib import Path
+
+    from viewephys.gui import EphysBinViewer, LFPackBinViewer
     from viewephys.viewer.qt import create_app
 
     app = create_app()
-    self = EphysBinViewer(args.file)  # noqa
+    # lfpack HDF5 archives need the LFPack-aware viewer; binaries use the base one.
+    is_h5 = args.file is not None and Path(args.file).suffix.lower() in (
+        ".h5",
+        ".hdf5",
+    )
+    ViewerClass = LFPackBinViewer if (args.lfpack or is_h5) else EphysBinViewer
+    self = ViewerClass(args.file)  # noqa
     sys.exit(app.exec())