{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Development"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2\n",
    "# import skimage.io\n",
    "# import matplotlib\n",
    "# import matplotlib.pyplot as plt\n",
    "# %matplotlib inline\n",
    "# nd2 = \"/home/dan/pims/pims/tests/data/bioformats/cluster.nd2\"\n",
    "from pathlib import Path\n",
    "\n",
    "import nima_io.read as ir\n",
    "\n",
    "tdata = Path(\"../../tests/data/\")\n",
    "\n",
    "lif = tdata / \"2015Aug28_TransHXB2_50min+DMSO.lif\"\n",
    "img_tile = tdata / \"t4_1.tif\"  # C=3 T=4 S=15\n",
    "img_void_tile = tdata / \"tile6_1.tif\"  # C=4 T=3 S=14 scattered\n",
    "# imgsingle = tdata / \"exp2_2.tif\"  # C=2 T=81\n",
    "\n",
    "# mcts = tdata / \"multi-channel-time-series.ome.tif\"  # C=3 T=7\n",
    "# bigtiff = tdata / \"LC26GFP_1.tf8\"  # bigtiff\n",
    "\n",
    "slif = str(lif)\n",
    "simg_tile = str(img_tile)\n",
    "simg_void_tile = str(img_void_tile)\n",
    "# simgsingle = str(imgsingle)\n",
    "# smcts = str(mcts)Z`Z\n",
    "# sbigtiff = str(bigtiff)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "Core metadata list at:\n",
    "https://docs.openmicroscopy.org/bio-formats/7.1.0/developers/file-reader.html\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "md, wr = ir.read(slif)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "wr.rdr.setSeries(4)\n",
    "wr.rdr.getImageCount()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "wr.rdr.getDimensionOrder()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "TODO: test convert value"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "ome_store = wr.rdr.getMetadataStore()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "## XML\n",
    "getRoot was used in imgread-0.2.1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "root = ome_store.getRoot()\n",
    "instrument = root.getInstrument(0)\n",
    "detector = instrument.getDetector(0)\n",
    "detector.getModel()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "wr.rdr.getMetadataStoreRoot().getInstrument(0).getDetector(0).getModel()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "wr.rdr.getMetadataStore().getRoot().getInstrument(0).getDetector(0).getModel()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "[m for m in root.__dir__() if m[:3] == \"get\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "image = root.getImage(3)\n",
    "[m for m in image.__dir__() if m[:3] == \"get\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "obj = image.getObjectiveSettings()\n",
    "[m for m in obj.__dir__() if m[:3] == \"get\"]\n",
    "obj.getID()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "pixels = image.getPixels()\n",
    "[m for m in pixels.__dir__() if m[:3] == \"get\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "scrolled": true,
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "ch = pixels.getChannel(0)\n",
    "[m for m in ch.__dir__() if m[:3] == \"get\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "lp = ch.getLightPath()\n",
    "[m for m in lp.__dir__() if m[:3] == \"get\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "pixels.getTimeIncrement()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "plane = pixels.getPlane(11)\n",
    "[m for m in plane.__dir__() if m[:3] == \"get\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "import jpype\n",
    "\n",
    "jpype.JObject(plane.getTheC()), plane.getDeltaT(), plane.getExposureTime()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "for k in root.__dir__():\n",
    "    if k[:3] == \"get\":\n",
    "        print(k)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "im = root.getImage(0)\n",
    "obj = im.getObjectiveSettings()\n",
    "(\n",
    "    obj.getID(),\n",
    "    obj.getMedium(),\n",
    "    obj.getRefractiveIndex(),\n",
    "    obj.getCorrectionCollar(),\n",
    "    obj.getObjective(),\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "(\n",
    "    wr.rdr.getMetadataStore().getObjectiveID(0, 0) == obj.getID(),\n",
    "    wr.rdr.getMetadataStore().getObjectiveLensNA(0, 0),\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "## md vs root (to remember)\n",
    "\n",
    "from md i can get info on camera, objectives ...\n",
    "\n",
    "but also key parameters like exposuretime, DeltaT, planePositionXYZ"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "md_vtile, wr_vtile = ir.read(simg_void_tile)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "wr_vtile.rdr.getMetadataStore().getObjectiveCount(0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "ome_store = wr_vtile.rdr.getMetadataStore()\n",
    "ome_store.getXMLAnnotationValue(\n",
    "    0\n",
    ") == ome_store.getRoot().getStructuredAnnotations().getXMLAnnotation(0).getValue()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "# import bioformats\n",
    "\n",
    "# md = bioformats.get_omexml_metadata(slif)\n",
    "from xml.etree import ElementTree as ET\n",
    "\n",
    "# mdroot = ET.fromstring(wr.rdr.getMetadataStore().dumpXML())\n",
    "java_string = (\n",
    "    wr_vtile.rdr.getMetadataStoreRoot()\n",
    "    .getStructuredAnnotations()\n",
    "    .getXMLAnnotation(0)\n",
    "    .getValue()\n",
    ")\n",
    "python_string = jpype.java.lang.String(java_string).toString()\n",
    "mdroot = ET.fromstring(python_string.getBytes())\n",
    "\n",
    "for a in mdroot:\n",
    "    print((a.tag, a.attrib))\n",
    "    for aa in a:\n",
    "        print((\" GGSSS \", aa.tag, aa.attrib))\n",
    "        for aaa in aa:\n",
    "            print((\" GGSSS2 \", aaa.tag, aaa.attrib))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "import xmltodict\n",
    "\n",
    "m1 = xmltodict.parse(ome_store.dumpXML().getBytes())\n",
    "list(m1[\"OME\"]), m1[\"OME\"][\"Instrument\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "metalist = [\n",
    "    (child.tag, [[child.attrib]])\n",
    "    for child in ET.fromstring(ome_store.dumpXML().getBytes()).iter()\n",
    "]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "m = metalist[10]\n",
    "m[0], m[1][0][0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "autoscroll": false,
    "ein.hycell": false,
    "ein.tags": "worksheet-0",
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "for child in mdroot:\n",
    "    if child.tag.endswith(\"\"):\n",
    "        for grandchild in child:\n",
    "            print((grandchild.tag, grandchild.attrib))"
   ]
  }
 ],
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   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.11.7"
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  "name": "general_reading_and_development.ipynb"
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