h5viewer 0.7.5

Viewer for hdf5 files created by labmate

Install

pip install h5viewer

or download the exe file from the last release. It was tested on mac and windows.

Usage

To open the viewer run h5viewer inside your cmd or run the executable file.

Run analysis

By default, analyze code will be executed with exec, which means:

• if you started the window from cmd it'll execute from the same cmd
• if you started the window as an exe file, it'll execute inside the virtual environment of this exe file, where almost nothing installed

If you want to run an analysis inside the specific environment, you should specify it at the beginning of the init_analyse.py file (which should be in the same directory as your data file).

Example for Mac:

# SOURCE: source ~/opt/anaconda3/bin/activate pyqt

Example for Windows:

# SOURCE: C:\ProgramData\Anaconda3\Scripts\activate.bat&&conda activate pyqt

How to run code before your analyze cell. init_analyse.py

If you want to set up any variables or imports before running the analysis_cell, you can do in by adding the init_analyse.py file in the same directory as the data file.

Use case: This is the classical file structure if you use labmate library:

• sample_001
  • analysis_code
    • analysis_script.py
  • data
    • experiment_1
      • init_analyse.py
      • data_file.h5 Suppose you opened data_file.h5 and try to run the code inside it, but it needs dependencies from analysis_script.py. So they could be imported inside init_analyse.py like this:

from labmate.acquisition_notebook import AcquisitionAnalysisManager

SCRIPT_DIR = os.path.join(os.path.dirname(__file__), os.pardir)
sys.path.append(os.path.join(os.path.abspath(SCRIPT_DIR), 'analyse'))

meas_dir = os.path.split(os.path.split(SCRIPT_DIR)[0])[0]
aqm = AcquisitionAnalysisManager(meas_dir)

from analysis_script import *

Error

Any error can be seen in the console view at the bottom right. Output from executing analysis_cell is also available there.

Set up AcquisitionAnalysisManager to create init_analyse.py automatically

There is no need for you to create an init_analyse.py file in each directory.

You can set any file to be an init_analyse.py by providing it to AcquisitionAnalysisManager:

aqm.set_init_analyse_file("some_init.py")

Dev

How to compile locally

Install pyinstaller

python -m pip install --upgrade pip
pip install setuptools wheel twine
pip install -r requirements.txt
pip install pyinstaller

Then run pyinstaller main.spec Depending on which system you are, it will create a program file for this system inside the dist

Note: there is no need to install the package with pip to compile it.

Installation in dev mode

You can download the code, package it and install it in dev mode. It will allow you to change the code while using it.

python setup.py bdist_wheel && pip install -e .

or you can just run

python setup.py develop