h5nuvola.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# H5 file viewer\n",
    "\n",
    "Workflow:<br/>\n",
    "  1. Browse a file  \n",
    "  2. Click \"Load File\" button\n",
    "  3. Click on tree objects to expand it and visualise its attributes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# imports and global variables\n",
    "from IPython.display import Javascript, HTML, display\n",
    "from ipywidgets import link, Layout, Tab, Box, HBox, VBox, IntSlider, FloatSlider, Text, Textarea, Label, Button, Image\n",
    "from traitlets import Int, Float, Unicode, List, Tuple, Bool\n",
    "from hdfviewer.widgets.PathSelector import PathSelector\n",
    "from ipytree import Tree, Node\n",
    "import h5py as h5\n",
    "\n",
    "import time\n",
    "\n",
    "h5_dict = {}\n",
    "h5_objects = []\n",
    "\n",
    "tree = Tree(multiple_selection=False)\n",
    "tree_dict = {}\n",
    "node_selected = None # current Node object selected\n",
    "\n",
    "# Text widget to display selected_node props and attrs\n",
    "name_text = Label(value = 'node selected')\n",
    "file_text = Label(value = 'file selected')\n",
    "dtype_text = Label()\n",
    "dshape_text = Label()\n",
    "attrs_text = Textarea(value = 'attributes displayed here',                      \n",
    "                      description = '',\n",
    "                      disabled = True,\n",
    "                      continous_update = True,\n",
    "                      layout = Layout(height = '50%', width = '100%')\n",
    "                     )\n",
    "tabs = Tab() # container with tabs\n",
    "\n",
    "# h5nuvola logo\n",
    "f_logo = open(\"./logo-h5nuvola.png\", \"rb\")\n",
    "image = f_logo.read()\n",
    "h5nuvola_logo_item = Image(value=image,\n",
    "                           format='png',\n",
    "                           width=285,\n",
    "                           height=60\n",
    "                          )\n",
    "h5nuvola_logo_item.layout.justify_content = 'center'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# define properties for each Node of the Tree\n",
    "class H5Obj(Node):\n",
    "    #name\n",
    "    #icon\n",
    "    tp = Unicode() # type - file, group or dataset\n",
    "    obj_filepath = Unicode()\n",
    "    obj_path = Unicode()\n",
    "    obj_attributes = List()\n",
    "    obj_children = Bool()\n",
    "    obj_dtype = Unicode()\n",
    "    obj_dshape = Tuple()\n",
    "\n",
    "# routine to create Tree\n",
    "def create_root_node(root_properties):\n",
    "    global tree\n",
    "    # create node\n",
    "    root_node = H5Obj(name = root_properties['h5_name'],                      \n",
    "                      icon = 'folder-o',\n",
    "                      tp = root_properties['type'],\n",
    "                      obj_filepath = root_properties['filepath'],\n",
    "                      obj_path = '/',\n",
    "                      obj_attributes = root_properties['attrs'],\n",
    "                      obj_children = root_properties['children'],\n",
    "                      obj_dtype = 'Group size',\n",
    "                      obj_dshape = (root_properties['group_size'],) # tuple\n",
    "                     )\n",
    "    # add node to the tree\n",
    "    tree.add_node(root_node)\n",
    "    \n",
    "    return root_node                      \n",
    "\n",
    "# routine to expand a Node of the Tree\n",
    "def expand_node(parent_node, new_items):\n",
    "    for i in range(len(new_items)):\n",
    "        # create new node\n",
    "        new_node = H5Obj(name = new_items[i]['name'].split('/')[-1],\n",
    "                         icon = new_items[i]['icon'],\n",
    "                         tp = new_items[i]['type'], # 'file', 'group', 'dataset'\n",
    "                         obj_filepath = parent_node.obj_filepath,\n",
    "                         obj_path = new_items[i]['name'],                         \n",
    "                         obj_children = new_items[i]['children'],\n",
    "                         obj_dtype = new_items[i]['dtype'],\n",
    "                         obj_dshape = new_items[i]['dshape'], # tuple\n",
    "                         obj_attributes = new_items[i]['attrs']\n",
    "                        )        \n",
    "        parent_node.add_node(new_node)\n",
    "\n",
    "    \n",
    "# aux h5 methods\n",
    "def h5_visit(name, obj):\n",
    "    global h5_objects    \n",
    "    h5_objects.append(obj)\n",
    "\n",
    "def h5_get_items(items):\n",
    "    items_list = [] # a list of dict containing all item's properties\n",
    "    for item in items:\n",
    "        name = item[1].name # str\n",
    "        tp = '' # str\n",
    "        icon = '' # str    \n",
    "        children = None # boolean\n",
    "        dtype = '' # str\n",
    "        dshape = () # tuple\n",
    "        attrs = [] # list\n",
    "        \n",
    "        if type(item[1]) == h5._hl.dataset.Dataset: # is dataset\n",
    "            tp = 'dataset'\n",
    "            icon = 'bars'\n",
    "            children = False\n",
    "            if h5.check_dtype(vlen=item[1].dtype) == bytes:\n",
    "                dtype = 'string'\n",
    "                dshape = (0,) # tuple\n",
    "            else:\n",
    "                dtype = str(item[1].dtype)\n",
    "                dshape = item[1].shape # tuple           \n",
    "        else: # is group\n",
    "            tp = 'group'\n",
    "            icon = 'folder-o'\n",
    "            if len(item[1].items()) == 0:\n",
    "                children = False\n",
    "            else:\n",
    "                children = True            \n",
    "            dtype = 'Group size'\n",
    "            dshape =  ( len(item[1].items()), ) # tuple\n",
    "        \n",
    "        # get attrs\n",
    "        if len(item[1].attrs.keys()) == 0: # if there is no attributes\n",
    "            pass\n",
    "        else:\n",
    "            for key in item[1].attrs.keys():\n",
    "                attrs.append({'attr_name':key,\n",
    "                              'attr_value':item[1].attrs[key].decode('utf-8')\n",
    "                             })\n",
    "        # set list        \n",
    "        items_list.append({'name': name,\n",
    "                           'type': tp,\n",
    "                           'icon': icon,                           \n",
    "                           'children': children,\n",
    "                           'dtype': dtype,\n",
    "                           'dshape': dshape,\n",
    "                           'attrs': attrs\n",
    "                          })\n",
    "    return items_list\n",
    "\n",
    "def set_attrs_text():\n",
    "    global node_selected\n",
    "    attrs_str = ''\n",
    "    for attr in node_selected.obj_attributes:    \n",
    "        attrs_str = attrs_str + attr['attr_name'] + ': ' + attr['attr_value'] + '\\n\\n'\n",
    "    return attrs_str"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Server side file browser\n",
    "#root_dir = '/run/user/1000/gvfs/sftp:host=tesla.elettra.eu,user=administrator/net/memory4twinmic/store/project/twinmic/scicomp/tesla-storage'\n",
    "root_dir = './'\n",
    "path = PathSelector(root_dir, \n",
    "                    extensions=[\".hdf\", \".h5\", \".nxs\", \".ptyd\", \".ptyr\"])\n",
    "\n",
    "# Button to load h5 file and add it to the Tree\n",
    "button_load = Button(\n",
    "    description = 'Load h5 file',\n",
    "    disabled = False,\n",
    "    button_style = '', # 'success', 'info', 'warning', 'danger' or ''\n",
    "    tooltip = 'Click to load the selected h5 file',\n",
    "    icon = ''\n",
    ")\n",
    "# Button to close h5 file and remove it from the Tree\n",
    "button_close = Button(\n",
    "    description = 'Close h5 file',\n",
    "    disabled = False,\n",
    "    button_style = '',\n",
    "    tooltip = 'Click to close the selected h5 file',\n",
    "    icon = ''\n",
    ")\n",
    "\n",
    "\n",
    "def on_button_load_clicked(btn_obj):\n",
    "    global h5_dict, hf_objects, h5_new_items\n",
    "    if path.path:\n",
    "        if path.path not in h5_dict:\n",
    "            print(\"Loading %s\"%(path.path))\n",
    "            hf = h5.File(path.path, 'r')\n",
    "            h5_dict[path.path] = {'hf': hf}\n",
    "            h5_name = str(hf.filename).split('/')[-1]\n",
    "            h5_dict[path.path]['h5_name'] = h5_name\n",
    "            h5_objects = []\n",
    "            hf.visititems(h5_visit)\n",
    "            h5_dict[path.path]['h5_objects'] = h5_objects\n",
    "            \n",
    "            # check if it has children\n",
    "            if len(hf.items()) == 0:\n",
    "                children = False\n",
    "            else:\n",
    "                children = True\n",
    "            \n",
    "            root_attrs = []\n",
    "            if len(hf.attrs.keys()) == 0:\n",
    "                pass\n",
    "            else:\n",
    "                for key in hf.attrs.keys():\n",
    "                    root_attrs.append([ key, hf.attrs[key].decode('utf-8') ])           \n",
    "            root_properties = {'h5_name': h5_name,\n",
    "                               'type': 'file',\n",
    "                               'filepath': path.path,\n",
    "                               'attrs': root_attrs,\n",
    "                               'children': children,\n",
    "                               'group_size': len(hf.items())\n",
    "                              }\n",
    "            h5_dict[path.path]['root_properties'] = root_properties\n",
    "            \n",
    "            # create Tree and retrieve root node created\n",
    "            tree_dict[h5_name] = create_root_node(root_properties)\n",
    "            # get new items\n",
    "            h5_new_items = h5_get_items(hf.items())\n",
    "            \n",
    "            if root_properties['children']:\n",
    "                expand_node(tree_dict[h5_name], h5_new_items)\n",
    "            \n",
    "            tabs.selected_index = 1\n",
    "                    \n",
    "        else:\n",
    "            print(\"File %s already opened\"%(path.path))\n",
    "    else:\n",
    "        print(\"Please select a file on the File Browser widget\")\n",
    "\n",
    "def on_button_close_clicked(btn_obj):\n",
    "    global h5_dict\n",
    "    print('Close h5 file')\n",
    "    # close h5 file object and delete from h5_dict\n",
    "    h5_dict[node_selected.obj_filepath]['hf'].close()\n",
    "    del h5_dict[node_selected.obj_filepath]\n",
    "    # remove from tree\n",
    "    tree.remove_node(node_selected)    \n",
    " \n",
    "button_load.on_click(on_button_load_clicked)\n",
    "button_close.on_click(on_button_close_clicked)\n",
    "\n",
    "# define and bind tree event handler\n",
    "def on_selected_change(change):\n",
    "    global node_selected, name_text, button_close, attrs_text\n",
    "    node_selected = change['new'][0]\n",
    "    if node_selected.obj_children and node_selected.nodes == (): # if node has children and have no nodes expand it\n",
    "        h5_new_items = h5_get_items( h5_dict[node_selected.obj_filepath]['hf'][node_selected.obj_path].items() )\n",
    "        expand_node(node_selected, h5_new_items)\n",
    "    if node_selected.tp != 'file':\n",
    "        button_close.disabled = True\n",
    "    else:\n",
    "        button_close.disabled = False\n",
    "    # update name_text, file_text\n",
    "    name_text.value = node_selected.obj_path\n",
    "    file_text.value = node_selected.obj_filepath\n",
    "    dtype_text.value = node_selected.obj_dtype\n",
    "    dshape_text.value = str(node_selected.obj_dshape)\n",
    "    # show attributes\n",
    "    attrs_text.value = set_attrs_text()\n",
    "    \n",
    "    \n",
    "tree.observe(on_selected_change, names='selected_nodes')\n",
    "\n",
    "# Display widgets\n",
    "# VBox([Label('Browser'), \n",
    "#       path.widget, \n",
    "#       button_load, \n",
    "#       HBox([ VBox([Label('TreeViewer'), tree]), VBox([Label('Selection'), Label('   '), Label('File'), HBox([file_text, button_close]), Label('Object'), name_text]) ]) ])\n",
    "\n",
    "# Layout and Display widgets - Using Flexbox\n",
    "tree.layout = Layout(width = '100%',\n",
    "                     height = '800px',\n",
    "                     overflow_x = 'scroll',\n",
    "                     overflow_y = 'scroll')\n",
    "# items for Flexbox\n",
    "file_browser_item = VBox([ Label('Browser'), path.widget, button_load, button_close ])\n",
    "tree_viewer_item = VBox([ Label('H5 Content'), tree ])\n",
    "attrs_item = VBox([Label('Selection'),\n",
    "                   Label('   '),\n",
    "                   Label('File'),\n",
    "                   file_text,\n",
    "                   Label('Object'),\n",
    "                   name_text,\n",
    "                   dtype_text,\n",
    "                   dshape_text,\n",
    "                   Label('Attributes'),\n",
    "                   attrs_text\n",
    "                  ])\n",
    "\n",
    "box_layout = Layout(display = 'flex', # 'inline-flex', 'flex'\n",
    "                    flex_flow = 'column nowrap', # 'column-reverse', 'column', 'row', 'row-reverse' | 'nowrap', 'wrap', 'wrap-reverse'\n",
    "                    justify_content = 'space-around', # 'flex-start', 'flex-end', 'center', 'space-between', 'space-around' \n",
    "                    align_items = 'stretch', # 'flex-start', 'flex-end', 'center', 'baseline', 'stretch'\n",
    "                    border = 'solid 10px rgb(0,130,196)',\n",
    "                    width = '100%'\n",
    "                   )\n",
    "\n",
    "hbox_layout = Layout(display = 'inline-flex',\n",
    "                     flex = '1 1 auto',\n",
    "                     flex_flow = 'row nowrap',\n",
    "                     justify_content = 'space-around',\n",
    "                     align_items = 'stretch',\n",
    "                     border = 'solid 1px black',\n",
    "                     width = '100%'\n",
    "                    )\n",
    "\n",
    "# children for Tabs\n",
    "children_tabs = [ file_browser_item, HBox([ tree_viewer_item, attrs_item ], layout = hbox_layout) ]\n",
    "\n",
    "# Trying Tabs\n",
    "tabs.children = children_tabs\n",
    "tabs.set_title(0, 'File Browser')\n",
    "tabs.set_title(1, 'H5 Content')\n",
    "\n",
    "#children = VBox([ h5nuvola_logo_item, HBox([file_browser_item, tree_viewer_item, attrs_plot_item], layout = hbox_layout) ])\n",
    "children = VBox([ h5nuvola_logo_item, tabs ])\n",
    "box = Box(children = [children],\n",
    "          layout = box_layout )\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
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       "Box(children=(VBox(children=(Image(value=b'\\x89PNG\\r\\n\\x1a\\n\\x00\\x00\\x00\\rIHDR\\x00\\x00\\x01\\x1d\\x00\\x00\\x00<\\x0…"
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   ],
   "source": [
    "box"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "# remove and add tabs in Tab() widget\n",
    "t = tabs.children\n",
    "t = list(t)\n",
    "del t[1]\n",
    "# t = tuple(t)\n",
    "tabs.children  = t"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [],
   "source": [
    "tabs.children = children_tabs"
   ]
  }
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