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Merge pull request #72 from kushalkolar/inscopix-importer
Inscopix importer
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docs/source/user_guides/viewer/modules/inscopix_importer.rst
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| .. _module_InscopixImporter: | ||
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| Inscopix Importer | ||
| ***************** | ||
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| The Inscopix Importer module can be used to open ``.isxd`` movies created by Inscopix acquisition software | ||
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| .. note:: You must have your own license for activating/running the Inscopix Data Processing Software (IDPS) and downloading the IDPS API and ``isx`` library. Mesmerize only provides an implementation of ``isx`` to read ``.isxd`` movies into the application. | ||
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| In order to use the importer you will need to add the path to the parent dir containing the ``isx`` library to your ``PYTHONPATH`` environment variable. | ||
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| For example if your ``isx`` dir is located at: | ||
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| ``` | ||
| /home/user/Inscopix Data Processing 1.6.0/Inscopix Data Processing.linux/Contents/API/Python/isx`` | ||
| ``` | ||
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| Then you will need to add the path to the parent dir, for example: | ||
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| ``` | ||
| export PYTHONPATH="/home/user/Inscopix Data Processing 1.6.0/Inscopix Data Processing.linux/Contents/API/Python:$PYTHONPATH" | ||
| ``` | ||
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| **Usage:** | ||
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| 1. Enter the path to the ``.isxd`` or click the ``...`` and choose the file. | ||
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| 2. Click the button to load the file into the :ref:`Viewer Work Environment <ViewerWorkEnv>`. | ||
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| The sampling rate (framerate) of the video is automatically imported from the ``isxd`` file. | ||
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| .. note:: Memory usage is quite high when loading files, you will need at least twice as much RAM as the size of the file you're trying to open. |
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| import isx | ||
| import numpy as np | ||
| import click | ||
| from multiprocessing import shared_memory | ||
| from tqdm import tqdm | ||
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| @click.command() | ||
| @click.option('--isx-path', type=str) | ||
| @click.option('--shm-meta-array-name', type=str) | ||
| def load_file(isx_path, shm_meta_array_name):#shm_name, shm-size, shm-dtype): | ||
| """ | ||
| isx_path: full path to the isx file to open | ||
| shm_meta_array_name: same of the shared memory array that is used to pass | ||
| array metadata (shape, dtype, name) to effectively communication with the | ||
| parent mesmerize instance | ||
| shm-name: name of the parent shared array that contains the | ||
| """ | ||
| movie = isx.Movie.read(isx_path) | ||
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| meta = movie.get_acquisition_info() | ||
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| d = \ | ||
| { | ||
| 'fps': 1000 / movie.timing.period.to_msecs(), | ||
| 'origin': meta['Microscope Type'], | ||
| 'date': '00000000_000000', | ||
| 'orig_meta': meta | ||
| } | ||
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| # total number of frames in the recording | ||
| nframes = movie.timing.num_samples | ||
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| # shape of each frame | ||
| frame0 = movie.get_frame_data(0) | ||
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| # image shape | ||
| shape = (*frame0.shape, nframes) | ||
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| # calculate number of bytes required for the shared memory | ||
| nbytes = np.prod(shape) * np.dtype(movie.data_type).itemsize | ||
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| # created a shared memory buffer | ||
| shm = shared_memory.SharedMemory(create=True, size=nbytes) | ||
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| # create shared numpy array backed by the shared memory buffer | ||
| imgseq = np.ndarray(shape, dtype=np.dtype(movie.data_type), buffer=shm.buf) | ||
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| # fill the array with the inscopix data | ||
| for i in tqdm(range(nframes)): | ||
| imgseq[..., i] = movie.get_frame_data(i) | ||
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| # communicate the array metadata to access the shared array from within mesmerize | ||
| shm_metadata = shared_memory.SharedMemory(name=shm_meta_array_name) | ||
| array_metadata = np.ndarray((5,), dtype=np.dtype('<U64'), buffer=shm_metadata.buf) | ||
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| array_metadata[0] = shm.name | ||
| array_metadata[1] = np.dtype(movie.data_type).name | ||
| array_metadata[2] = ','.join(str(s) for s in shape) | ||
| array_metadata[3] = str(d['fps']) | ||
| array_metadata[4] = str(d['origin']) | ||
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| print(f'imgdata address: {shm.name}') | ||
| print(array_metadata) | ||
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| shm.close() | ||
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| if __name__ == '__main__': | ||
| load_file() | ||
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| import numpy as np | ||
| from ...common.qdialogs import * | ||
| from ..core.common import ViewerUtils | ||
| from PyQt5 import QtWidgets | ||
| from ..core import ViewerWorkEnv | ||
| from ..core.data_types import ImgData | ||
| from multiprocessing.shared_memory import SharedMemory | ||
| import os | ||
| from subprocess import Popen | ||
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| class Widget(QtWidgets.QWidget): | ||
| def __init__(self, parent): | ||
| QtWidgets.QWidget.__init__(self, parent=parent) | ||
| self.vboxlayout = QtWidgets.QVBoxLayout(self) | ||
| self.hboxlayout = QtWidgets.QHBoxLayout(self) | ||
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| self.label_choose_file = QtWidgets.QLabel() | ||
| self.label_choose_file.setText("Choose `.isxd` file") | ||
| self.vboxlayout.addWidget(self.label_choose_file) | ||
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| self.line_edit_path = QtWidgets.QLineEdit() | ||
| self.line_edit_path.setPlaceholderText("Path to `.isxd` file") | ||
| self.line_edit_path.returnPressed.connect(self.parent().load_file) | ||
| self.hboxlayout.addWidget(self.line_edit_path) | ||
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| self.btn_open_file_dialog = QtWidgets.QPushButton() | ||
| self.btn_open_file_dialog.setText("...") | ||
| self.btn_open_file_dialog.clicked.connect(self.parent().file_dialog) | ||
| self.hboxlayout.addWidget(self.btn_open_file_dialog) | ||
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| self.vboxlayout.addLayout(self.hboxlayout) | ||
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| self.btn_load_file = QtWidgets.QPushButton() | ||
| self.btn_load_file.setText("Load File") | ||
| self.btn_load_file.clicked.connect(self.parent().load_file) | ||
| self.vboxlayout.addWidget(self.btn_load_file) | ||
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| class ModuleGUI(QtWidgets.QDockWidget): | ||
| def __init__(self, parent, viewer_reference): | ||
| self.vi = ViewerUtils(viewer_reference) | ||
| QtWidgets.QDockWidget.__init__(self, parent) | ||
| self.setFloating(True) | ||
| self.setWindowTitle('Inscopix Importer') | ||
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| self.widget = Widget(parent=self) | ||
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| self.setWidget(self.widget) | ||
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| # self.setLayout(self.vboxlayout) | ||
| @use_open_file_dialog("Choose .isxd file", "", exts=["*.isxd"]) | ||
| def file_dialog(self, path, *args, **kwargs): | ||
| self.widget.line_edit_path.setText(path) | ||
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| @present_exceptions("File open error", "The following error occurred when opening the file") | ||
| def load_file(self, *args, **kwargs): | ||
| shm = SharedMemory(create=True, size=5 * np.dtype('<U64').itemsize) | ||
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| # get array metadata, shared memory buffer name, dtype, and shape | ||
| array_metadata = np.ndarray(shape=(5,), dtype=np.dtype('<U64'), buffer=shm.buf) | ||
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| importer_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), '_inscopix_importer.py') | ||
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| file_path = self.widget.line_edit_path.text() | ||
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| cmd = ['python', importer_path, '--isx-path', file_path, '--shm-meta-array-name', shm.name] | ||
| print(cmd) | ||
| proc = Popen( | ||
| cmd, | ||
| env=os.environ.copy() | ||
| ) | ||
| proc.wait() | ||
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| # read the metadata | ||
| name = array_metadata[0] | ||
| dtype = array_metadata[1] | ||
| shape = array_metadata[2] | ||
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| # open the shared buffer | ||
| existing_shm = SharedMemory(name=array_metadata[0]) | ||
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| shape = tuple(map(int, shape.split(','))) | ||
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| _imgseq = np.ndarray(shape, dtype=np.dtype(dtype), buffer=existing_shm.buf) | ||
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| imgseq = np.zeros(shape=shape, dtype=np.dtype(dtype)) | ||
| imgseq[:] = _imgseq[:] | ||
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| d = \ | ||
| { | ||
| 'fps': float(array_metadata[3]), | ||
| 'origin': array_metadata[4], | ||
| 'date': '00000000_000000' | ||
| } | ||
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| imgdata = ImgData(imgseq, d) | ||
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| self.vi.viewer.workEnv = ViewerWorkEnv(imgdata) | ||
| self.vi.update_workEnv() | ||
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| existing_shm.close() | ||
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