Example_flat notebook

Example_flat.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Example of making sky flat"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import reducer.astro_gui as astro_gui\n",
+    "import reducer.gui\n",
+    "from reducer.image_browser import ImageBrowser\n",
+    "import os\n",
+    "from ccdproc import ImageFileCollection"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Here we set up the directories for the example data."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# To use the sample data set:\n",
+    "data_dir = reducer.notebook_dir.get_data_path()\n",
+    "\n",
+    "# Or, uncomment line below and modify as needed\n",
+    "# data_dir = 'path/to/your/data'\n",
+    "# example_dir is where the master_dark and master_bias are put in\n",
+    "# destination_dir is set default to example_dir\n",
+    "\n",
+    "example_dir = os.path.join(os.path.dirname(os.path.abspath(reducer.__file__)), 'data')\n",
+    "destination_dir = example_dir"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "images = ImageFileCollection(location=data_dir, keywords='*')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Now we will do reduction for flat frames, then try to combine them to a master flat.  \n",
+    "There are already existed master_bias and master_dark files in example_dir. You have to subtract both during reduction process.\n",
+    "### Procedure:\n",
+    "\n",
+    "Check `Subtract bias` and select `Created in this notebook`  \n",
+    "Check `Subtract dark` and select `Created in this notebook` and also `Scale dark by exposure time`  \n",
+    "Then press `Lock settings and Go!`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "49d527f41d934eeb9eba46d6f47f7d83",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/html": [
+       "<p>Failed to display Jupyter Widget of type <code>Reduction</code>.</p>\n",
+       "<p>\n",
+       "  If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n",
+       "  that the widgets JavaScript is still loading. If this message persists, it\n",
+       "  likely means that the widgets JavaScript library is either not installed or\n",
+       "  not enabled. See the <a href=\"https://ipywidgets.readthedocs.io/en/stable/user_install.html\">Jupyter\n",
+       "  Widgets Documentation</a> for setup instructions.\n",
+       "</p>\n",
+       "<p>\n",
+       "  If you're reading this message in another frontend (for example, a static\n",
+       "  rendering on GitHub or <a href=\"https://nbviewer.jupyter.org/\">NBViewer</a>),\n",
+       "  it may mean that your frontend doesn't currently support widgets.\n",
+       "</p>\n"
+      ],
+      "text/plain": [
+       "Reduction(children=(Box(children=(ToggleButton(value=False, description='Reduce flat frames'),)), VBox(children=(CopyFiles(children=(Box(children=(CheckboxPlus(children=(Label(value='Copy without any other action?'), Checkbox(value=False, style=DescriptionStyle(description_width='initial'))), layout=Layout(align_items='center', display='flex', justify_content='flex-start')),)), VBox(layout=Layout(display='none', visibility='hidden')), Checkbox(value=True, layout=Layout(display='none', visibility='hidden')))), Overscan(children=(Box(children=(CheckboxPlus(children=(Label(value='Subtract overscan?'), Checkbox(value=False, style=DescriptionStyle(description_width='initial'))), layout=Layout(align_items='center', display='flex', justify_content='flex-start')),)), VBox(children=(AxisSelection(children=(HBox(children=(Label(value='Region is all of'), ToggleButtons(options=OrderedDict([('axis 0', 0), ('axis 1', 1)]), style=ToggleButtonsStyle(button_width='initial'), value=0)), layout=Layout(align_items='center')), Label(value='and along the other axis from '), IntText(value=0, style=DescriptionStyle(description_width='initial')), Label(value='up to (but not including):'), IntText(value=0, style=DescriptionStyle(description_width='initial'))), layout=Layout(display='flex')), ToggleContainer(children=(Box(children=(CheckboxPlus(children=(Label(value='Fit polynomial to overscan?'), Checkbox(value=False, style=DescriptionStyle(description_width='initial'))), layout=Layout(align_items='center', display='flex', justify_content='flex-start')),)), VBox(children=(PolynomialDropdown(description='Choose fit', options=OrderedDict([('Order 0/one term (constant)', 1), ('Order 1/two term (linear)', 2), ('Order 2/three team (quadratic)', 3), ('Are you serious? Higher order is silly.', None)]), value=1),), layout=Layout(display='none', visibility='hidden')), Checkbox(value=True, layout=Layout(display='none', visibility='hidden'))))), layout=Layout(display='none', visibility='hidden')), Checkbox(value=True, layout=Layout(display='none', visibility='hidden')))), Trim(children=(Box(children=(CheckboxPlus(children=(Label(value='Trim (specify region to keep)?'), Checkbox(value=False, style=DescriptionStyle(description_width='initial'))), layout=Layout(align_items='center', display='flex', justify_content='flex-start')),)), VBox(children=(AxisSelection(children=(HBox(children=(Label(value='Region is all of'), ToggleButtons(options=OrderedDict([('axis 0', 0), ('axis 1', 1)]), style=ToggleButtonsStyle(button_width='initial'), value=0)), layout=Layout(align_items='center')), Label(value='and along the other axis from '), IntText(value=0, style=DescriptionStyle(description_width='initial')), Label(value='up to (but not including):'), IntText(value=3073, style=DescriptionStyle(description_width='initial'))), layout=Layout(display='flex')),), layout=Layout(display='none', visibility='hidden')), Checkbox(value=True, layout=Layout(display='none', visibility='hidden')))), BiasSubtract(children=(Box(children=(CheckboxPlus(children=(Label(value='Subtract bias?'), Checkbox(value=False, style=DescriptionStyle(description_width='initial'))), layout=Layout(align_items='center', display='flex', justify_content='flex-start')),)), VBox(children=(MasterImageSource(children=(ToggleButtons(description='Source:', options=(('Created in this notebook', 'notebook'), ('File on disk', 'disk')), value='notebook'), Dropdown(description='Select file:', layout=Layout(display='none'), options=('Not working yet',), value='Not working yet'))),), layout=Layout(display='none', visibility='hidden')), Checkbox(value=True, layout=Layout(display='none', visibility='hidden')))), DarkSubtract(children=(Box(children=(CheckboxPlus(children=(Label(value='Subtract Dark?'), Checkbox(value=False, style=DescriptionStyle(description_width='initial'))), layout=Layout(align_items='center', display='flex', justify_content='flex-start')),)), VBox(children=(MasterImageSource(children=(ToggleButtons(description='Source:', options=(('Created in this notebook', 'notebook'), ('File on disk', 'disk')), value='notebook'), Dropdown(description='Select file:', layout=Layout(display='none'), options=('Not working yet',), value='Not working yet'))), DarkScaleSetting(children=(ToggleButtons(description='Scale dark by exposure time (if needed)', index=1, options={'Yes': True, 'No': False}, value=False),))), layout=Layout(display='none', visibility='hidden')), Checkbox(value=True, layout=Layout(display='none', visibility='hidden'))))), layout=Layout(display='none', visibility='hidden')), Checkbox(value=True, layout=Layout(display='none', visibility='hidden')), HBox(children=(Button(description='Lock settings and Go!', disabled=True, layout=Layout(display='none'), style=ButtonStyle()), Button(description='Unlock settings', disabled=True, layout=Layout(display='none'), style=ButtonStyle()))), Box(children=(FloatProgress(value=0.0, layout=Layout(display='none'), max=1.0),))))"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Reduce flat frames Yes\n",
+      "\tCopy without any other action? No\n",
+      "\tSubtract overscan? No\n",
+      "\tTrim (specify region to keep)? No\n",
+      "\tSubtract bias? Yes\n",
+      "\t\tSource: notebook\n",
+      "\tSubtract Dark? Yes\n",
+      "\t\tSource: notebook\n",
+      "\t\tScale dark by exposure time (if needed): True\n"
+     ]
+    }
+   ],
+   "source": [
+    "reduced_collection = ImageFileCollection(location=destination_dir, keywords='*')\n",
+    "flat_reduction = astro_gui.Reduction(description='Reduce flat frames',\n",
+    "                                     toggle_type='button',\n",
+    "                                     allow_bias=True,\n",
+    "                                     master_source=reduced_collection,\n",
+    "                                     allow_dark=True,\n",
+    "                                     allow_flat=False,\n",
+    "                                     input_image_collection=images,\n",
+    "                                     destination=destination_dir,\n",
+    "                                     apply_to={'imagetyp': 'flat'})\n",
+    "\n",
+    "flat_reduction.display()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Procedure:\n",
+    "\n",
+    "Check `Clip before combining` and select `Sigma clip` with **low threshold**: 2, **high threshold**: 4  \n",
+    "Check `Combine images` with **Median** combination method, and select `Scale before combining` with **median**  \n",
+    "Then press `Lock settings and Go!`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "54c19d68609d45bfb4d33f72ce4eb1d5",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/html": [
+       "<p>Failed to display Jupyter Widget of type <code>Combiner</code>.</p>\n",
+       "<p>\n",
+       "  If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n",
+       "  that the widgets JavaScript is still loading. If this message persists, it\n",
+       "  likely means that the widgets JavaScript library is either not installed or\n",
+       "  not enabled. See the <a href=\"https://ipywidgets.readthedocs.io/en/stable/user_install.html\">Jupyter\n",
+       "  Widgets Documentation</a> for setup instructions.\n",
+       "</p>\n",
+       "<p>\n",
+       "  If you're reading this message in another frontend (for example, a static\n",
+       "  rendering on GitHub or <a href=\"https://nbviewer.jupyter.org/\">NBViewer</a>),\n",
+       "  it may mean that your frontend doesn't currently support widgets.\n",
+       "</p>\n"
+      ],
+      "text/plain": [
+       "Combiner(children=(Box(children=(ToggleButton(value=False, description='Make Master Flat'),)), VBox(children=(Clipping(children=(Box(children=(CheckboxPlus(children=(Label(value='Clip before combining?'), Checkbox(value=False, style=DescriptionStyle(description_width='initial'))), layout=Layout(align_items='center', display='flex', justify_content='flex-start')),), layout=Layout(padding='3px')), VBox(children=(ToggleMinMax(children=(Box(children=(CheckboxPlus(children=(Label(value='Clip by min/max?'), Checkbox(value=False, style=DescriptionStyle(description_width='initial'))), layout=Layout(align_items='center', display='flex', justify_content='flex-start')),), layout=Layout(padding='3px')), VBox(children=(FloatText(value=0.0, description='Low threshold', layout=Layout(width='10em'), style=DescriptionStyle(description_width='initial')), FloatText(value=0.0, description='High threshold', layout=Layout(width='10em'), style=DescriptionStyle(description_width='initial'))), layout=Layout(display='none', justify_content='space-around', padding='0px 0px 0px 30px', visibility='hidden', width='50%')), Checkbox(value=True, layout=Layout(display='none', visibility='hidden')))), ToggleMinMax(children=(Box(children=(CheckboxPlus(children=(Label(value='Sigma clip?'), Checkbox(value=False, style=DescriptionStyle(description_width='initial'))), layout=Layout(align_items='center', display='flex', justify_content='flex-start')),), layout=Layout(padding='3px')), VBox(children=(FloatText(value=0.0, description='Low threshold', layout=Layout(width='10em'), style=DescriptionStyle(description_width='initial')), FloatText(value=0.0, description='High threshold', layout=Layout(width='10em'), style=DescriptionStyle(description_width='initial'))), layout=Layout(display='none', justify_content='space-around', padding='0px 0px 0px 30px', visibility='hidden', width='50%')), Checkbox(value=True, layout=Layout(display='none', visibility='hidden'))))), layout=Layout(display='none', padding='0px 0px 0px 30px', visibility='hidden')), Checkbox(value=True, layout=Layout(display='none', visibility='hidden')))), Combine(children=(Box(children=(CheckboxPlus(children=(Label(value='Combine images?'), Checkbox(value=False, style=DescriptionStyle(description_width='initial'))), layout=Layout(align_items='center', display='flex', justify_content='flex-start')),)), VBox(children=(ToggleButtons(description='Combination method:', options=('Average', 'Median'), style=ToggleButtonsStyle(description_width='initial'), value='Average'), ToggleContainer(children=(Box(children=(CheckboxPlus(children=(Label(value='Scale before combining?'), Checkbox(value=False, style=DescriptionStyle(description_width='initial'))), layout=Layout(align_items='center', display='flex', justify_content='flex-start')),)), VBox(children=(RadioButtons(description='Which should scale to same value?', options=('mean', 'median'), style=DescriptionStyle(description_width='initial'), value='mean'),), layout=Layout(display='none', visibility='hidden')), Checkbox(value=True, layout=Layout(display='none', visibility='hidden'))))), layout=Layout(display='none', visibility='hidden')), Checkbox(value=True, layout=Layout(display='none', visibility='hidden')))), GroupBy(children=(Box(children=(CheckboxPlus(children=(Label(value='Group by:'), Checkbox(value=True, style=DescriptionStyle(description_width='initial'))), layout=Layout(align_items='center', display='flex', justify_content='flex-start')),)), VBox(children=(Text(value='exposure, filter', description='Keywords (comma-separated)', style=DescriptionStyle(description_width='initial')),), layout=Layout(visibility='visible')), Checkbox(value=False, layout=Layout(display='none', visibility='hidden'))))), layout=Layout(display='none', visibility='hidden')), Checkbox(value=True, layout=Layout(display='none', visibility='hidden')), HBox(children=(Button(description='Lock settings and Go!', disabled=True, layout=Layout(display='none'), style=ButtonStyle()), Button(description='Unlock settings', disabled=True, layout=Layout(display='none'), style=ButtonStyle()))), Box(children=(FloatProgress(value=0.0, layout=Layout(display='none'), max=1.0),))))"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Make Master Flat Yes\n",
+      "\tClip before combining? Yes\n",
+      "\t\tClip by min/max? No\n",
+      "\t\tSigma clip? Yes\n",
+      "\t\t\tLow threshold: 2.0\n",
+      "\t\t\tHigh threshold: 4.0\n",
+      "\tCombine images? Yes\n",
+      "\t\tCombination method:: Median\n",
+      "\t\tScale before combining? Yes\n",
+      "\t\t\tWhich should scale to same value?: median\n",
+      "\tGroup by: No\n"
+     ]
+    }
+   ],
+   "source": [
+    "reduced_collection = ImageFileCollection(location=destination_dir, keywords='*')\n",
+    "\n",
+    "flat = astro_gui.Combiner(description=\"Make Master Flat\",\n",
+    "                          toggle_type='button',\n",
+    "                          file_name_base='master_flat',\n",
+    "                          group_by='exposure, filter',\n",
+    "                          image_source=reduced_collection,\n",
+    "                          apply_to={'imagetyp': 'flat'},\n",
+    "                          destination=destination_dir)\n",
+    "flat.display()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Now you can find master flat in the destination directory"
+   ]
+  }
+ ],
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+}