Convert us-ALEX SM files to Photon-HDF5.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
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   },
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   "source": [
    "filename = r'C:\\Data\\Antonio\\Eitan\\022rde11_T_minus15_acc__NT_plus10_don_1.sm'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "import matplotlib.pyplot as plt\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import phconvert as phc\n",
    "phc.__version__"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Author"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "author = 'Eitan Lerner'\n",
    "author_affiliation = 'UCLA'\n",
    "creator = 'Antonino Ingargiola'\n",
    "creator_affiliation = 'UCLA'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Sample"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "comment = 'A demostrative smFRET-usALEX measurement.'\n",
    "sample_name = '022rde11_T_minus15_acc__NT_plus10_don_1'\n",
    "dye_names = ['ATTO550', 'ATTO647N']\n",
    "buffer_name = 'Transcription buffer.'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Prepare data\n",
    "\n",
    "## Read the data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "d = phc.loader.usalex_sm(filename,\n",
    "                         donor = 0,\n",
    "                         acceptor = 1,\n",
    "                         alex_period = 4000,\n",
    "                         alex_period_donor = (2850, 580),\n",
    "                         alex_period_acceptor = (930, 2580),\n",
    "                         excitation_wavelengths = (532e-9, 635e-9),\n",
    "                         detection_wavelengths = (580e-9, 680e-9))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "phc.plotter.alternation_hist(d)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Add author and sample info"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "d['comment'] = comment\n",
    "\n",
    "d['sample'] = dict(\n",
    "    sample_name=sample_name,\n",
    "    dye_names=[n.encode() for n in dye_names],\n",
    "    buffer_name=buffer_name,\n",
    "    num_dyes = len(dye_names))\n",
    "\n",
    "d['identity'] = dict(\n",
    "    author=author,\n",
    "    author_affiliation=author_affiliation,\n",
    "    creator=creator,\n",
    "    creator_affiliation=creator_affiliation)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Validate the Photon-HDF5 structure\n",
    "\n",
    "Before writing to disk, we assure the file structure follows the Photon-HDF5 format:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "phc.hdf5.assert_valid_photon_hdf5(d)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Save to Photon-HDF5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "phc.hdf5.save_photon_hdf5(d)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "d['_data_file'].close()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Load Photon-HDF5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from pprint import pprint"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "filename = d['_data_file'].filename\n",
    "#filename = r'C:\\Data\\Antonio\\Eitan\\022rde11_T_minus15_acc__NT_plus10_don_1_new_copy.hdf5'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "h5data = phc.hdf5.load_photon_hdf5(filename)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "phc.hdf5.dict_from_group(h5data.identity)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "phc.hdf5.dict_from_group(h5data.setup)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "pprint(phc.hdf5.dict_from_group(h5data.photon_data))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": []
  }
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