From 62b0abed5ef49465566d363699cb044e7d5f73e3 Mon Sep 17 00:00:00 2001 From: Rob Firth Date: Tue, 12 Dec 2017 16:03:12 +0000 Subject: [PATCH] fixing Issue #28 and probably #24 too --- notebooks/Filter Integration Bughunt.ipynb | 8620 +++++++++++++++++ .../Tutorials/1 - pycoco calling CoCo.ipynb | 1154 +-- 2 files changed, 8838 insertions(+), 936 deletions(-) create mode 100644 notebooks/Filter Integration Bughunt.ipynb diff --git a/notebooks/Filter Integration Bughunt.ipynb b/notebooks/Filter Integration Bughunt.ipynb new file mode 100644 index 0000000..b22154d --- /dev/null +++ b/notebooks/Filter Integration Bughunt.ipynb @@ -0,0 +1,8620 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "I get the following output from the code below:\n", + "```\n", + "SN2006aj_53786.270000\n", + "Filter_area = 958.904702526\n", + "Integrated flux = 65.3955702281\n", + "SN2006aj_53787.230000\n", + "Filter_area = 583.185950131\n", + "Integrated flux = 41.0298233406\n", + "SN2006aj_53788.200000\n", + "Filter_area = 1358.72907164\n", + "Integrated flux = 131.886385781\n", + "SN2006aj_53789.170000\n", + "Filter_area = 1357.72217486\n", + "Integrated flux = 146.521717503\n", + "SN2006aj_53790.140000\n", + "Filter_area = 1361.80653493\n", + "Integrated flux = 164.34213622\n", + "SN2006aj_53791.100000\n", + "Filter_area = 1356.94789874\n", + "Integrated flux = 163.802182486\n", + "SN2006aj_53792.070000\n", + "Filter_area = 1358.08475139\n", + "Integrated flux = 170.17603978\n", + "SN2006aj_53793.040000\n", + "Filter_area = 1342.63870674\n", + "Integrated flux = 156.866851118\n", + "SN2006aj_53794.010000\n", + "Filter_area = 1358.55873129\n", + "Integrated flux = 160.605022385\n", + "SN2006aj_53794.970000\n", + "Filter_area = 494.406955809\n", + "Integrated flux = 64.3739416067\n", + "SN2006aj_53795.940000\n", + "Filter_area = 1315.20012487\n", + "Integrated flux = 137.109302356\n", + "SN2006aj_53796.910000\n", + "Filter_area = 1313.60589901\n", + "Integrated flux = 121.107583058\n", + "SN2006aj_53797.880000\n", + "Filter_area = 1313.47758368\n", + "Integrated flux = 110.196456176\n", + "SN2006aj_53798.840000\n", + "Filter_area = 1315.40072684\n", + "Integrated flux = 92.2847571523\n", + "SN2006aj_53799.810000\n", + "Filter_area = 1314.80756892\n", + "Integrated flux = 91.8528874753\n", + "SN2006aj_53801.750000\n", + "Filter_area = 1298.16443106\n", + "Integrated flux = 63.0384962734\n", + "SN2006aj_53802.720000\n", + "Filter_area = 1299.82908919\n", + "Integrated flux = 45.3544694847\n", + "SN2006aj_53803.680000\n", + "Filter_area = 1296.91402526\n", + "Integrated flux = 37.1949955268\n", + "SN2006aj_53803.680001\n", + "Filter_area = 1296.93821395\n", + "Integrated flux = 51.5059756933```\n", + "\n", + "Notice something weird - the filter area is changing. The filter area shouldn't change. Suspect that it might be to do with the resampling of the filter response, but the fluctuations are severe - around 1300 for most, but as low as 494 for SN2006aj_53794.970000." + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "%matplotlib notebook\n", + "\n", + "from matplotlib import pyplot as plt\n", + "\n", + "import os\n", + "import numpy as np\n", + "from astropy.table import Table\n", + "\n", + "import pycoco as pcc" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "application/javascript": [ + "/* Put everything inside the global mpl namespace */\n", + "window.mpl = {};\n", + "\n", + "\n", + "mpl.get_websocket_type = function() {\n", + " if (typeof(WebSocket) !== 'undefined') {\n", + " return WebSocket;\n", + " } else if (typeof(MozWebSocket) !== 'undefined') {\n", + " return MozWebSocket;\n", + " } else {\n", + " alert('Your browser does not have WebSocket support.' +\n", + " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", + " 'Firefox 4 and 5 are also supported but you ' +\n", + " 'have to enable WebSockets in about:config.');\n", + " };\n", + "}\n", + "\n", + "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", + " this.id = figure_id;\n", + "\n", + " this.ws = websocket;\n", + "\n", + " this.supports_binary = (this.ws.binaryType != undefined);\n", + "\n", + " if (!this.supports_binary) {\n", + " var warnings = document.getElementById(\"mpl-warnings\");\n", + " if (warnings) {\n", + " warnings.style.display = 'block';\n", + " warnings.textContent = (\n", + " \"This browser does not support binary websocket messages. \" +\n", + " \"Performance may be slow.\");\n", + " }\n", + " }\n", + "\n", + " this.imageObj = new Image();\n", + "\n", + " this.context = undefined;\n", + " this.message = undefined;\n", + " this.canvas = undefined;\n", + " this.rubberband_canvas = undefined;\n", + " this.rubberband_context = undefined;\n", + " this.format_dropdown = undefined;\n", + "\n", + " this.image_mode = 'full';\n", + "\n", + " this.root = $('
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')\n", + " nav_element.attr('style', 'width: 100%');\n", + " this.root.append(nav_element);\n", + "\n", + " // Define a callback function for later on.\n", + " function toolbar_event(event) {\n", + " return fig.toolbar_button_onclick(event['data']);\n", + " }\n", + " function toolbar_mouse_event(event) {\n", + " return fig.toolbar_button_onmouseover(event['data']);\n", + " }\n", + "\n", + " for(var toolbar_ind in mpl.toolbar_items) {\n", + " var name = mpl.toolbar_items[toolbar_ind][0];\n", + " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", + " var image = mpl.toolbar_items[toolbar_ind][2];\n", + " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", + "\n", + " if (!name) {\n", + " // put a spacer in here.\n", + " continue;\n", + " }\n", + " var button = $('');\n", + " button.click(method_name, toolbar_event);\n", + " button.mouseover(tooltip, toolbar_mouse_event);\n", + " nav_element.append(button);\n", + " }\n", + "\n", + " // Add the status bar.\n", + " var status_bar = $('');\n", + " nav_element.append(status_bar);\n", + " this.message = status_bar[0];\n", + "\n", + " // Add the close button to the window.\n", + " var buttongrp = $('
');\n", + " var button = $('');\n", + " button.click(function (evt) { fig.handle_close(fig, {}); } );\n", + " button.mouseover('Stop Interaction', toolbar_mouse_event);\n", + " buttongrp.append(button);\n", + " var titlebar = this.root.find($('.ui-dialog-titlebar'));\n", + " titlebar.prepend(buttongrp);\n", + "}\n", + "\n", + "mpl.figure.prototype._root_extra_style = function(el){\n", + " var fig = this\n", + " el.on(\"remove\", function(){\n", + "\tfig.close_ws(fig, {});\n", + " });\n", + "}\n", + "\n", + "mpl.figure.prototype._canvas_extra_style = function(el){\n", + " // this is important to make the div 'focusable\n", + " el.attr('tabindex', 0)\n", + " // reach out to IPython and tell the keyboard manager to turn it's self\n", + " // off when our div gets focus\n", + "\n", + " // location in version 3\n", + " if (IPython.notebook.keyboard_manager) {\n", + " IPython.notebook.keyboard_manager.register_events(el);\n", + " }\n", + " else {\n", + " // location in version 2\n", + " IPython.keyboard_manager.register_events(el);\n", + " }\n", + "\n", + "}\n", + "\n", + "mpl.figure.prototype._key_event_extra = function(event, name) {\n", + " var manager = IPython.notebook.keyboard_manager;\n", + " if (!manager)\n", + " manager = IPython.keyboard_manager;\n", + "\n", + " // Check for shift+enter\n", + " if (event.shiftKey && event.which == 13) {\n", + " this.canvas_div.blur();\n", + " event.shiftKey = false;\n", + " // Send a \"J\" for go to next cell\n", + " event.which = 74;\n", + " event.keyCode = 74;\n", + " manager.command_mode();\n", + " manager.handle_keydown(event);\n", + " }\n", + "}\n", + "\n", + "mpl.figure.prototype.handle_save = function(fig, msg) {\n", + " fig.ondownload(fig, null);\n", + "}\n", + "\n", + "\n", + "mpl.find_output_cell = function(html_output) {\n", + " // Return the cell and output element which can be found *uniquely* in the notebook.\n", + " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", + " // IPython event is triggered only after the cells have been serialised, which for\n", + " // our purposes (turning an active figure into a static one), is too late.\n", + " var cells = IPython.notebook.get_cells();\n", + " var ncells = cells.length;\n", + " for (var i=0; i= 3 moved mimebundle to data attribute of output\n", + " data = data.data;\n", + " }\n", + " if (data['text/html'] == html_output) {\n", + " return [cell, data, j];\n", + " }\n", + " }\n", + " }\n", + " }\n", + "}\n", + "\n", + "// Register the function which deals with the matplotlib target/channel.\n", + "// The kernel may be null if the page has been refreshed.\n", + "if (IPython.notebook.kernel != null) {\n", + " IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n", + "}\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "path_to_filter = os.path.join(pcc.defaults._default_filter_dir_path,\"BessellB.dat\")\n", + "BessellB = pcc.classes.FilterClass()\n", + "BessellB.read_filter_file(path_to_filter)\n", + "BessellB.calculate_AB_zp()\n", + "BessellB.plot()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "the resample_response at this point looks like this:\n", + "\n", + "```python\n", + "def resample_response(self, new_wavelength = False, k = 1, verbose=False,\n", + " *args, **kwargs):\n", + " \"\"\"\n", + " Bit dodgy - spline has weird results for poorly sampled filters.\n", + " Now the order is by default 1, seems to be less likely to introduce artifacts\n", + "\n", + " Parameters\n", + " ----------\n", + "\n", + " Returns\n", + " -------\n", + " \"\"\"\n", + "\n", + " if hasattr(self, \"wavelength\") and hasattr(self, \"throughput\"):\n", + "\n", + " if verbose: print(\"resampling response\")\n", + "\n", + " self._wavelength_orig = self.wavelength\n", + " self._throughput_orig = self.throughput\n", + "\n", + " self.wavelength = np.concatenate(([0,1], self._wavelength_orig, [24999,25000]))\n", + " self.throughput = np.concatenate(([0,0], self._throughput_orig, [0,0]))\n", + "\n", + " interp_func = InterpolatedUnivariateSpline(self.wavelength, self.throughput, k = k,\n", + " *args, **kwargs)\n", + " self.throughput = interp_func(new_wavelength)\n", + " self.wavelength = new_wavelength\n", + " # self.wavelength.name = \"wavelength\"\n", + "\n", + " self.throughput[np.where(self.throughput < 0.0)] = 0.0\n", + " else:\n", + " warning.warn(\"Doesn't look like you have loaded a filter into the object\")\n", + "```\n", + "\n", + "... that docstring does _not_ inspire confidence, does it. Need to be a bit more careful. However, with the concatenation, it should be the case that there are throughput zeros at both extremes of the wavelength - in the messed up example, this is clearly not the case." + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "application/javascript": [ + "/* Put everything inside the global mpl namespace */\n", + "window.mpl = {};\n", + "\n", + "\n", + "mpl.get_websocket_type = function() {\n", + " if (typeof(WebSocket) !== 'undefined') {\n", + " return WebSocket;\n", + " } else if (typeof(MozWebSocket) !== 'undefined') {\n", + " return MozWebSocket;\n", + " } else {\n", + " alert('Your browser does not have WebSocket support.' +\n", + " 'Please try Chrome, Safari or Firefox ≥ 6. 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');\n", + " var titletext = $(\n", + " '
');\n", + " titlebar.append(titletext)\n", + " this.root.append(titlebar);\n", + " this.header = titletext[0];\n", + "}\n", + "\n", + "\n", + "\n", + "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", + "\n", + "}\n", + "\n", + "\n", + "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", + "\n", + "}\n", + "\n", + "mpl.figure.prototype._init_canvas = function() {\n", + " var fig = this;\n", + "\n", + " var canvas_div = $('
');\n", + "\n", + " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", + "\n", + " function canvas_keyboard_event(event) {\n", + " return fig.key_event(event, event['data']);\n", + " }\n", + "\n", + " canvas_div.keydown('key_press', canvas_keyboard_event);\n", + " canvas_div.keyup('key_release', canvas_keyboard_event);\n", + " this.canvas_div = canvas_div\n", + " this._canvas_extra_style(canvas_div)\n", + " this.root.append(canvas_div);\n", + "\n", + " var canvas = $('');\n", + " canvas.addClass('mpl-canvas');\n", + " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", + "\n", + " this.canvas = canvas[0];\n", + " this.context = canvas[0].getContext(\"2d\");\n", + "\n", + " var backingStore = this.context.backingStorePixelRatio ||\n", + "\tthis.context.webkitBackingStorePixelRatio ||\n", + "\tthis.context.mozBackingStorePixelRatio ||\n", + "\tthis.context.msBackingStorePixelRatio ||\n", + "\tthis.context.oBackingStorePixelRatio ||\n", + "\tthis.context.backingStorePixelRatio || 1;\n", + "\n", + " mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n", + "\n", + " var rubberband = $('');\n", + " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", + "\n", + " var pass_mouse_events = true;\n", + "\n", + " canvas_div.resizable({\n", + " start: function(event, ui) {\n", + " pass_mouse_events = false;\n", + " },\n", + " resize: function(event, ui) {\n", + " fig.request_resize(ui.size.width, ui.size.height);\n", + " },\n", + " stop: function(event, ui) {\n", + " pass_mouse_events = true;\n", + " fig.request_resize(ui.size.width, ui.size.height);\n", + " },\n", + " });\n", + "\n", + " function mouse_event_fn(event) {\n", + " if (pass_mouse_events)\n", + " return fig.mouse_event(event, event['data']);\n", + " }\n", + "\n", + " rubberband.mousedown('button_press', mouse_event_fn);\n", + " rubberband.mouseup('button_release', mouse_event_fn);\n", + " // Throttle sequential mouse events to 1 every 20ms.\n", + " rubberband.mousemove('motion_notify', mouse_event_fn);\n", + "\n", + " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", + " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", + "\n", + " canvas_div.on(\"wheel\", function (event) {\n", + " event = event.originalEvent;\n", + " event['data'] = 'scroll'\n", + " if (event.deltaY < 0) {\n", + " event.step = 1;\n", + " } else {\n", + " event.step = -1;\n", + " }\n", + " mouse_event_fn(event);\n", + " });\n", + "\n", + " canvas_div.append(canvas);\n", + " canvas_div.append(rubberband);\n", + "\n", + " this.rubberband = rubberband;\n", + " this.rubberband_canvas = rubberband[0];\n", + " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", + " this.rubberband_context.strokeStyle = \"#000000\";\n", + "\n", + " this._resize_canvas = function(width, height) {\n", + " // Keep the size of the canvas, canvas container, and rubber band\n", + " // canvas in synch.\n", + " canvas_div.css('width', width)\n", + " canvas_div.css('height', height)\n", + "\n", + " canvas.attr('width', width * mpl.ratio);\n", + " canvas.attr('height', height * mpl.ratio);\n", + " canvas.attr('style', 'width: ' + width + 'px; height: ' + height + 'px;');\n", + "\n", + " rubberband.attr('width', width);\n", + " rubberband.attr('height', height);\n", + " }\n", + "\n", + " // Set the figure to an initial 600x600px, this will subsequently be updated\n", + " // upon first draw.\n", + " this._resize_canvas(600, 600);\n", + "\n", + " // Disable right mouse context menu.\n", + " $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n", + " return false;\n", + " });\n", + "\n", + " function set_focus () {\n", + " canvas.focus();\n", + " canvas_div.focus();\n", + " }\n", + "\n", + " window.setTimeout(set_focus, 100);\n", + "}\n", + "\n", + "mpl.figure.prototype._init_toolbar = function() {\n", + " var fig = this;\n", + "\n", + " var nav_element = $('
')\n", + " nav_element.attr('style', 'width: 100%');\n", + " this.root.append(nav_element);\n", + "\n", + " // Define a callback function for later on.\n", + " function toolbar_event(event) {\n", + " return fig.toolbar_button_onclick(event['data']);\n", + " }\n", + " function toolbar_mouse_event(event) {\n", + " return fig.toolbar_button_onmouseover(event['data']);\n", + " }\n", + "\n", + " for(var toolbar_ind in mpl.toolbar_items) {\n", + " var name = mpl.toolbar_items[toolbar_ind][0];\n", + " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", + " var image = mpl.toolbar_items[toolbar_ind][2];\n", + " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", + "\n", + " if (!name) {\n", + " // put a spacer in here.\n", + " continue;\n", + " }\n", + " var button = $('');\n", + " button.click(method_name, toolbar_event);\n", + " button.mouseover(tooltip, toolbar_mouse_event);\n", + " nav_element.append(button);\n", + " }\n", + "\n", + " // Add the status bar.\n", + " var status_bar = $('');\n", + " nav_element.append(status_bar);\n", + " this.message = status_bar[0];\n", + "\n", + " // Add the close button to the window.\n", + " var buttongrp = $('
');\n", + " var button = $('');\n", + " button.click(function (evt) { fig.handle_close(fig, {}); } );\n", + " button.mouseover('Stop Interaction', toolbar_mouse_event);\n", + " buttongrp.append(button);\n", + " var titlebar = this.root.find($('.ui-dialog-titlebar'));\n", + " titlebar.prepend(buttongrp);\n", + "}\n", + "\n", + "mpl.figure.prototype._root_extra_style = function(el){\n", + " var fig = this\n", + " el.on(\"remove\", function(){\n", + "\tfig.close_ws(fig, {});\n", + " });\n", + "}\n", + "\n", + "mpl.figure.prototype._canvas_extra_style = function(el){\n", + " // this is important to make the div 'focusable\n", + " el.attr('tabindex', 0)\n", + " // reach out to IPython and tell the keyboard manager to turn it's self\n", + " // off when our div gets focus\n", + "\n", + " // location in version 3\n", + " if (IPython.notebook.keyboard_manager) {\n", + " IPython.notebook.keyboard_manager.register_events(el);\n", + " }\n", + " else {\n", + " // location in version 2\n", + " IPython.keyboard_manager.register_events(el);\n", + " }\n", + "\n", + "}\n", + "\n", + "mpl.figure.prototype._key_event_extra = function(event, name) {\n", + " var manager = IPython.notebook.keyboard_manager;\n", + " if (!manager)\n", + " manager = IPython.keyboard_manager;\n", + "\n", + " // Check for shift+enter\n", + " if (event.shiftKey && event.which == 13) {\n", + " this.canvas_div.blur();\n", + " event.shiftKey = false;\n", + " // Send a \"J\" for go to next cell\n", + " event.which = 74;\n", + " event.keyCode = 74;\n", + " manager.command_mode();\n", + " manager.handle_keydown(event);\n", + " }\n", + "}\n", + "\n", + "mpl.figure.prototype.handle_save = function(fig, msg) {\n", + " fig.ondownload(fig, null);\n", + "}\n", + "\n", + "\n", + "mpl.find_output_cell = function(html_output) {\n", + " // Return the cell and output element which can be found *uniquely* in the notebook.\n", + " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", + " // IPython event is triggered only after the cells have been serialised, which for\n", + " // our purposes (turning an active figure into a static one), is too late.\n", + " var cells = IPython.notebook.get_cells();\n", + " var ncells = cells.length;\n", + " for (var i=0; i= 3 moved mimebundle to data attribute of output\n", + " data = data.data;\n", + " }\n", + " if (data['text/html'] == html_output) {\n", + " return [cell, data, j];\n", + " }\n", + " }\n", + " }\n", + " }\n", + "}\n", + "\n", + "// Register the function which deals with the matplotlib target/channel.\n", + "// The kernel may be null if the page has been refreshed.\n", + "if (IPython.notebook.kernel != null) {\n", + " IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n", + "}\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "path_to_filter = os.path.join(pcc.defaults._default_filter_dir_path,\"BessellB.dat\")\n", + "BessellB = pcc.classes.FilterClass()\n", + "BessellB.read_filter_file(path_to_filter)\n", + "BessellB.calculate_AB_zp()\n", + "BessellB.plot()\n", + "print(BessellB._effective_area)\n", + "print(pcc.kcorr.calc_filter_area(filter_object=BessellB))\n", + "print(pcc.kcorr.calc_filter_area(filter_name=\"BessellB\"))\n", + "BessellB.plot()" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "application/javascript": [ + "/* Put everything inside the global mpl namespace */\n", + "window.mpl = {};\n", + "\n", + "\n", + "mpl.get_websocket_type = function() {\n", + " if (typeof(WebSocket) !== 'undefined') {\n", + " return WebSocket;\n", + " } else if (typeof(MozWebSocket) !== 'undefined') {\n", + " return MozWebSocket;\n", + " } else {\n", + " alert('Your browser does not have WebSocket support.' +\n", + " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", + " 'Firefox 4 and 5 are also supported but you ' +\n", + " 'have to enable WebSockets in about:config.');\n", + " };\n", + "}\n", + "\n", + "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", + " this.id = figure_id;\n", + "\n", + " this.ws = websocket;\n", + "\n", + " this.supports_binary = (this.ws.binaryType != undefined);\n", + "\n", + " if (!this.supports_binary) {\n", + " var warnings = document.getElementById(\"mpl-warnings\");\n", + " if (warnings) {\n", + " warnings.style.display = 'block';\n", + " warnings.textContent = (\n", + " \"This browser does not support binary websocket messages. \" +\n", + " \"Performance may be slow.\");\n", + " }\n", + " }\n", + "\n", + " this.imageObj = new Image();\n", + "\n", + " this.context = undefined;\n", + " this.message = undefined;\n", + " this.canvas = undefined;\n", + " this.rubberband_canvas = undefined;\n", + " this.rubberband_context = undefined;\n", + " this.format_dropdown = undefined;\n", + "\n", + " this.image_mode = 'full';\n", + "\n", + " this.root = $('
');\n", + " this._root_extra_style(this.root)\n", + " this.root.attr('style', 'display: inline-block');\n", + "\n", + " $(parent_element).append(this.root);\n", + "\n", + " this._init_header(this);\n", + " this._init_canvas(this);\n", + " this._init_toolbar(this);\n", + "\n", + " var fig = this;\n", + "\n", + " this.waiting = false;\n", + "\n", + " this.ws.onopen = function () {\n", + " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", + " fig.send_message(\"send_image_mode\", {});\n", + " if (mpl.ratio != 1) {\n", + " fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n", + " }\n", + " fig.send_message(\"refresh\", {});\n", + " }\n", + "\n", + " this.imageObj.onload = function() {\n", + " if (fig.image_mode == 'full') {\n", + " // Full images could contain transparency (where diff images\n", + " // almost always do), so we need to clear the canvas so that\n", + " // there is no ghosting.\n", + " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", + " }\n", + " fig.context.drawImage(fig.imageObj, 0, 0);\n", + " };\n", + "\n", + " this.imageObj.onunload = function() {\n", + " fig.ws.close();\n", + " }\n", + "\n", + " this.ws.onmessage = this._make_on_message_function(this);\n", + "\n", + " this.ondownload = ondownload;\n", + "}\n", + "\n", + "mpl.figure.prototype._init_header = function() {\n", + " var titlebar = $(\n", + " '
');\n", + " var titletext = $(\n", + " '
');\n", + " titlebar.append(titletext)\n", + " this.root.append(titlebar);\n", + " this.header = titletext[0];\n", + "}\n", + "\n", + "\n", + "\n", + "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", + "\n", + "}\n", + "\n", + "\n", + "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", + "\n", + "}\n", + "\n", + "mpl.figure.prototype._init_canvas = function() {\n", + " var fig = this;\n", + "\n", + " var canvas_div = $('
');\n", + "\n", + " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", + "\n", + " function canvas_keyboard_event(event) {\n", + " return fig.key_event(event, event['data']);\n", + " }\n", + "\n", + " canvas_div.keydown('key_press', canvas_keyboard_event);\n", + " canvas_div.keyup('key_release', canvas_keyboard_event);\n", + " this.canvas_div = canvas_div\n", + " this._canvas_extra_style(canvas_div)\n", + " this.root.append(canvas_div);\n", + "\n", + " var canvas = $('');\n", + " canvas.addClass('mpl-canvas');\n", + " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", + "\n", + " this.canvas = canvas[0];\n", + " this.context = canvas[0].getContext(\"2d\");\n", + "\n", + " var backingStore = this.context.backingStorePixelRatio ||\n", + "\tthis.context.webkitBackingStorePixelRatio ||\n", + "\tthis.context.mozBackingStorePixelRatio ||\n", + "\tthis.context.msBackingStorePixelRatio ||\n", + "\tthis.context.oBackingStorePixelRatio ||\n", + "\tthis.context.backingStorePixelRatio || 1;\n", + "\n", + " mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n", + "\n", + " var rubberband = $('');\n", + " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", + "\n", + " var pass_mouse_events = true;\n", + "\n", + " canvas_div.resizable({\n", + " start: function(event, ui) {\n", + " pass_mouse_events = false;\n", + " },\n", + " resize: function(event, ui) {\n", + " fig.request_resize(ui.size.width, ui.size.height);\n", + " },\n", + " stop: function(event, ui) {\n", + " pass_mouse_events = true;\n", + " fig.request_resize(ui.size.width, ui.size.height);\n", + " },\n", + " });\n", + "\n", + " function mouse_event_fn(event) {\n", + " if (pass_mouse_events)\n", + " return fig.mouse_event(event, event['data']);\n", + " }\n", + "\n", + " rubberband.mousedown('button_press', mouse_event_fn);\n", + " rubberband.mouseup('button_release', mouse_event_fn);\n", + " // Throttle sequential mouse events to 1 every 20ms.\n", + " rubberband.mousemove('motion_notify', mouse_event_fn);\n", + "\n", + " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", + " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", + "\n", + " canvas_div.on(\"wheel\", function (event) {\n", + " event = event.originalEvent;\n", + " event['data'] = 'scroll'\n", + " if (event.deltaY < 0) {\n", + " event.step = 1;\n", + " } else {\n", + " event.step = -1;\n", + " }\n", + " mouse_event_fn(event);\n", + " });\n", + "\n", + " canvas_div.append(canvas);\n", + " canvas_div.append(rubberband);\n", + "\n", + " this.rubberband = rubberband;\n", + " this.rubberband_canvas = rubberband[0];\n", + " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", + " this.rubberband_context.strokeStyle = \"#000000\";\n", + "\n", + " this._resize_canvas = function(width, height) {\n", + " // Keep the size of the canvas, canvas container, and rubber band\n", + " // canvas in synch.\n", + " canvas_div.css('width', width)\n", + " canvas_div.css('height', height)\n", + "\n", + " canvas.attr('width', width * mpl.ratio);\n", + " canvas.attr('height', height * mpl.ratio);\n", + " canvas.attr('style', 'width: ' + width + 'px; height: ' + height + 'px;');\n", + "\n", + " rubberband.attr('width', width);\n", + " rubberband.attr('height', height);\n", + " }\n", + "\n", + " // Set the figure to an initial 600x600px, this will subsequently be updated\n", + " // upon first draw.\n", + " this._resize_canvas(600, 600);\n", + "\n", + " // Disable right mouse context menu.\n", + " $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n", + " return false;\n", + " });\n", + "\n", + " function set_focus () {\n", + " canvas.focus();\n", + " canvas_div.focus();\n", + " }\n", + "\n", + " window.setTimeout(set_focus, 100);\n", + "}\n", + "\n", + "mpl.figure.prototype._init_toolbar = function() {\n", + " var fig = this;\n", + "\n", + " var nav_element = $('
')\n", + " nav_element.attr('style', 'width: 100%');\n", + " this.root.append(nav_element);\n", + "\n", + " // Define a callback function for later on.\n", + " function toolbar_event(event) {\n", + " return fig.toolbar_button_onclick(event['data']);\n", + " }\n", + " function toolbar_mouse_event(event) {\n", + " return fig.toolbar_button_onmouseover(event['data']);\n", + " }\n", + "\n", + " for(var toolbar_ind in mpl.toolbar_items) {\n", + " var name = mpl.toolbar_items[toolbar_ind][0];\n", + " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", + " var image = mpl.toolbar_items[toolbar_ind][2];\n", + " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", + "\n", + " if (!name) {\n", + " // put a spacer in here.\n", + " continue;\n", + " }\n", + " var button = $('');\n", + " button.click(method_name, toolbar_event);\n", + " button.mouseover(tooltip, toolbar_mouse_event);\n", + " nav_element.append(button);\n", + " }\n", + "\n", + " // Add the status bar.\n", + " var status_bar = $('');\n", + " nav_element.append(status_bar);\n", + " this.message = status_bar[0];\n", + "\n", + " // Add the close button to the window.\n", + " var buttongrp = $('
');\n", + " var button = $('');\n", + " button.click(function (evt) { fig.handle_close(fig, {}); } );\n", + " button.mouseover('Stop Interaction', toolbar_mouse_event);\n", + " buttongrp.append(button);\n", + " var titlebar = this.root.find($('.ui-dialog-titlebar'));\n", + " titlebar.prepend(buttongrp);\n", + "}\n", + "\n", + "mpl.figure.prototype._root_extra_style = function(el){\n", + " var fig = this\n", + " el.on(\"remove\", function(){\n", + "\tfig.close_ws(fig, {});\n", + " });\n", + "}\n", + "\n", + "mpl.figure.prototype._canvas_extra_style = function(el){\n", + " // this is important to make the div 'focusable\n", + " el.attr('tabindex', 0)\n", + " // reach out to IPython and tell the keyboard manager to turn it's self\n", + " // off when our div gets focus\n", + "\n", + " // location in version 3\n", + " if (IPython.notebook.keyboard_manager) {\n", + " IPython.notebook.keyboard_manager.register_events(el);\n", + " }\n", + " else {\n", + " // location in version 2\n", + " IPython.keyboard_manager.register_events(el);\n", + " }\n", + "\n", + "}\n", + "\n", + "mpl.figure.prototype._key_event_extra = function(event, name) {\n", + " var manager = IPython.notebook.keyboard_manager;\n", + " if (!manager)\n", + " manager = IPython.keyboard_manager;\n", + "\n", + " // Check for shift+enter\n", + " if (event.shiftKey && event.which == 13) {\n", + " this.canvas_div.blur();\n", + " event.shiftKey = false;\n", + " // Send a \"J\" for go to next cell\n", + " event.which = 74;\n", + " event.keyCode = 74;\n", + " manager.command_mode();\n", + " manager.handle_keydown(event);\n", + " }\n", + "}\n", + "\n", + "mpl.figure.prototype.handle_save = function(fig, msg) {\n", + " fig.ondownload(fig, null);\n", + "}\n", + "\n", + "\n", + "mpl.find_output_cell = function(html_output) {\n", + " // Return the cell and output element which can be found *uniquely* in the notebook.\n", + " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", + " // IPython event is triggered only after the cells have been serialised, which for\n", + " // our purposes (turning an active figure into a static one), is too late.\n", + " var cells = IPython.notebook.get_cells();\n", + " var ncells = cells.length;\n", + " for (var i=0; i= 3 moved mimebundle to data attribute of output\n", + " data = data.data;\n", + " }\n", + " if (data['text/html'] == html_output) {\n", + " return [cell, data, j];\n", + " }\n", + " }\n", + " }\n", + " }\n", + "}\n", + "\n", + "// Register the function which deals with the matplotlib target/channel.\n", + "// The kernel may be null if the page has been refreshed.\n", + "if (IPython.notebook.kernel != null) {\n", + " IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n", + "}\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "958.897101114\n", + "958.897101114\n", + "958.897101114\n" + ] + } + ], + "source": [ + "BessellB.resample_response(new_wavelength=np.arange(4500.0,9000.0, 1.0))\n", + "BessellB.plot()\n", + "print(BessellB._effective_area)\n", + "print(pcc.kcorr.calc_filter_area(filter_object=BessellB))\n", + "print(pcc.kcorr.calc_filter_area(filter_name=\"BessellB\"))" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "application/javascript": [ + "/* Put everything inside the global mpl namespace */\n", + "window.mpl = {};\n", + "\n", + "\n", + "mpl.get_websocket_type = function() {\n", + " if (typeof(WebSocket) !== 'undefined') {\n", + " return WebSocket;\n", + " } else if (typeof(MozWebSocket) !== 'undefined') {\n", + " return MozWebSocket;\n", + " } else {\n", + " alert('Your browser does not have WebSocket support.' +\n", + " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", + " 'Firefox 4 and 5 are also supported but you ' +\n", + " 'have to enable WebSockets in about:config.');\n", + " };\n", + "}\n", + "\n", + "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", + " this.id = figure_id;\n", + "\n", + " this.ws = websocket;\n", + "\n", + " this.supports_binary = (this.ws.binaryType != undefined);\n", + "\n", + " if (!this.supports_binary) {\n", + " var warnings = document.getElementById(\"mpl-warnings\");\n", + " if (warnings) {\n", + " warnings.style.display = 'block';\n", + " warnings.textContent = (\n", + " \"This browser does not support binary websocket messages. \" +\n", + " \"Performance may be slow.\");\n", + " }\n", + " }\n", + "\n", + " this.imageObj = new Image();\n", + "\n", + " this.context = undefined;\n", + " this.message = undefined;\n", + " this.canvas = undefined;\n", + " this.rubberband_canvas = undefined;\n", + " this.rubberband_context = undefined;\n", + " this.format_dropdown = undefined;\n", + "\n", + " this.image_mode = 'full';\n", + "\n", + " this.root = $('
');\n", + " this._root_extra_style(this.root)\n", + " this.root.attr('style', 'display: inline-block');\n", + "\n", + " $(parent_element).append(this.root);\n", + "\n", + " this._init_header(this);\n", + " this._init_canvas(this);\n", + " this._init_toolbar(this);\n", + "\n", + " var fig = this;\n", + "\n", + " this.waiting = false;\n", + "\n", + " this.ws.onopen = function () {\n", + " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", + " fig.send_message(\"send_image_mode\", {});\n", + " if (mpl.ratio != 1) {\n", + " fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n", + " }\n", + " fig.send_message(\"refresh\", {});\n", + " }\n", + "\n", + " this.imageObj.onload = function() {\n", + " if (fig.image_mode == 'full') {\n", + " // Full images could contain transparency (where diff images\n", + " // almost always do), so we need to clear the canvas so that\n", + " // there is no ghosting.\n", + " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", + " }\n", + " fig.context.drawImage(fig.imageObj, 0, 0);\n", + " };\n", + "\n", + " this.imageObj.onunload = function() {\n", + " fig.ws.close();\n", + " }\n", + "\n", + " this.ws.onmessage = this._make_on_message_function(this);\n", + "\n", + " this.ondownload = ondownload;\n", + "}\n", + "\n", + "mpl.figure.prototype._init_header = function() {\n", + " var titlebar = $(\n", + " '
');\n", + " var titletext = $(\n", + " '
');\n", + " titlebar.append(titletext)\n", + " this.root.append(titlebar);\n", + " this.header = titletext[0];\n", + "}\n", + "\n", + "\n", + "\n", + "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", + "\n", + "}\n", + "\n", + "\n", + "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", + "\n", + "}\n", + "\n", + "mpl.figure.prototype._init_canvas = function() {\n", + " var fig = this;\n", + "\n", + " var canvas_div = $('
');\n", + "\n", + " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", + "\n", + " function canvas_keyboard_event(event) {\n", + " return fig.key_event(event, event['data']);\n", + " }\n", + "\n", + " canvas_div.keydown('key_press', canvas_keyboard_event);\n", + " canvas_div.keyup('key_release', canvas_keyboard_event);\n", + " this.canvas_div = canvas_div\n", + " this._canvas_extra_style(canvas_div)\n", + " this.root.append(canvas_div);\n", + "\n", + " var canvas = $('');\n", + " canvas.addClass('mpl-canvas');\n", + " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", + "\n", + " this.canvas = canvas[0];\n", + " this.context = canvas[0].getContext(\"2d\");\n", + "\n", + " var backingStore = this.context.backingStorePixelRatio ||\n", + "\tthis.context.webkitBackingStorePixelRatio ||\n", + "\tthis.context.mozBackingStorePixelRatio ||\n", + "\tthis.context.msBackingStorePixelRatio ||\n", + "\tthis.context.oBackingStorePixelRatio ||\n", + "\tthis.context.backingStorePixelRatio || 1;\n", + "\n", + " mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n", + "\n", + " var rubberband = $('');\n", + " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", + "\n", + " var pass_mouse_events = true;\n", + "\n", + " canvas_div.resizable({\n", + " start: function(event, ui) {\n", + " pass_mouse_events = false;\n", + " },\n", + " resize: function(event, ui) {\n", + " fig.request_resize(ui.size.width, ui.size.height);\n", + " },\n", + " stop: function(event, ui) {\n", + " pass_mouse_events = true;\n", + " fig.request_resize(ui.size.width, ui.size.height);\n", + " },\n", + " });\n", + "\n", + " function mouse_event_fn(event) {\n", + " if (pass_mouse_events)\n", + " return fig.mouse_event(event, event['data']);\n", + " }\n", + "\n", + " rubberband.mousedown('button_press', mouse_event_fn);\n", + " rubberband.mouseup('button_release', mouse_event_fn);\n", + " // Throttle sequential mouse events to 1 every 20ms.\n", + " rubberband.mousemove('motion_notify', mouse_event_fn);\n", + "\n", + " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", + " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", + "\n", + " canvas_div.on(\"wheel\", function (event) {\n", + " event = event.originalEvent;\n", + " event['data'] = 'scroll'\n", + " if (event.deltaY < 0) {\n", + " event.step = 1;\n", + " } else {\n", + " event.step = -1;\n", + " }\n", + " mouse_event_fn(event);\n", + " });\n", + "\n", + " canvas_div.append(canvas);\n", + " canvas_div.append(rubberband);\n", + "\n", + " this.rubberband = rubberband;\n", + " this.rubberband_canvas = rubberband[0];\n", + " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", + " this.rubberband_context.strokeStyle = \"#000000\";\n", + "\n", + " this._resize_canvas = function(width, height) {\n", + " // Keep the size of the canvas, canvas container, and rubber band\n", + " // canvas in synch.\n", + " canvas_div.css('width', width)\n", + " canvas_div.css('height', height)\n", + "\n", + " canvas.attr('width', width * mpl.ratio);\n", + " canvas.attr('height', height * mpl.ratio);\n", + " canvas.attr('style', 'width: ' + width + 'px; height: ' + height + 'px;');\n", + "\n", + " rubberband.attr('width', width);\n", + " rubberband.attr('height', height);\n", + " }\n", + "\n", + " // Set the figure to an initial 600x600px, this will subsequently be updated\n", + " // upon first draw.\n", + " this._resize_canvas(600, 600);\n", + "\n", + " // Disable right mouse context menu.\n", + " $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n", + " return false;\n", + " });\n", + "\n", + " function set_focus () {\n", + " canvas.focus();\n", + " canvas_div.focus();\n", + " }\n", + "\n", + " window.setTimeout(set_focus, 100);\n", + "}\n", + "\n", + "mpl.figure.prototype._init_toolbar = function() {\n", + " var fig = this;\n", + "\n", + " var nav_element = $('
')\n", + " nav_element.attr('style', 'width: 100%');\n", + " this.root.append(nav_element);\n", + "\n", + " // Define a callback function for later on.\n", + " function toolbar_event(event) {\n", + " return fig.toolbar_button_onclick(event['data']);\n", + " }\n", + " function toolbar_mouse_event(event) {\n", + " return fig.toolbar_button_onmouseover(event['data']);\n", + " }\n", + "\n", + " for(var toolbar_ind in mpl.toolbar_items) {\n", + " var name = mpl.toolbar_items[toolbar_ind][0];\n", + " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", + " var image = mpl.toolbar_items[toolbar_ind][2];\n", + " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", + "\n", + " if (!name) {\n", + " // put a spacer in here.\n", + " continue;\n", + " }\n", + " var button = $('');\n", + " button.click(method_name, toolbar_event);\n", + " button.mouseover(tooltip, toolbar_mouse_event);\n", + " nav_element.append(button);\n", + " }\n", + "\n", + " // Add the status bar.\n", + " var status_bar = $('');\n", + " nav_element.append(status_bar);\n", + " this.message = status_bar[0];\n", + "\n", + " // Add the close button to the window.\n", + " var buttongrp = $('
');\n", + " var button = $('');\n", + " button.click(function (evt) { fig.handle_close(fig, {}); } );\n", + " button.mouseover('Stop Interaction', toolbar_mouse_event);\n", + " buttongrp.append(button);\n", + " var titlebar = this.root.find($('.ui-dialog-titlebar'));\n", + " titlebar.prepend(buttongrp);\n", + "}\n", + "\n", + "mpl.figure.prototype._root_extra_style = function(el){\n", + " var fig = this\n", + " el.on(\"remove\", function(){\n", + "\tfig.close_ws(fig, {});\n", + " });\n", + "}\n", + "\n", + "mpl.figure.prototype._canvas_extra_style = function(el){\n", + " // this is important to make the div 'focusable\n", + " el.attr('tabindex', 0)\n", + " // reach out to IPython and tell the keyboard manager to turn it's self\n", + " // off when our div gets focus\n", + "\n", + " // location in version 3\n", + " if (IPython.notebook.keyboard_manager) {\n", + " IPython.notebook.keyboard_manager.register_events(el);\n", + " }\n", + " else {\n", + " // location in version 2\n", + " IPython.keyboard_manager.register_events(el);\n", + " }\n", + "\n", + "}\n", + "\n", + "mpl.figure.prototype._key_event_extra = function(event, name) {\n", + " var manager = IPython.notebook.keyboard_manager;\n", + " if (!manager)\n", + " manager = IPython.keyboard_manager;\n", + "\n", + " // Check for shift+enter\n", + " if (event.shiftKey && event.which == 13) {\n", + " this.canvas_div.blur();\n", + " event.shiftKey = false;\n", + " // Send a \"J\" for go to next cell\n", + " event.which = 74;\n", + " event.keyCode = 74;\n", + " manager.command_mode();\n", + " manager.handle_keydown(event);\n", + " }\n", + "}\n", + "\n", + "mpl.figure.prototype.handle_save = function(fig, msg) {\n", + " fig.ondownload(fig, null);\n", + "}\n", + "\n", + "\n", + "mpl.find_output_cell = function(html_output) {\n", + " // Return the cell and output element which can be found *uniquely* in the notebook.\n", + " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", + " // IPython event is triggered only after the cells have been serialised, which for\n", + " // our purposes (turning an active figure into a static one), is too late.\n", + " var cells = IPython.notebook.get_cells();\n", + " var ncells = cells.length;\n", + " for (var i=0; i= 3 moved mimebundle to data attribute of output\n", + " data = data.data;\n", + " }\n", + " if (data['text/html'] == html_output) {\n", + " return [cell, data, j];\n", + " }\n", + " }\n", + " }\n", + " }\n", + "}\n", + "\n", + "// Register the function which deals with the matplotlib target/channel.\n", + "// The kernel may be null if the page has been refreshed.\n", + "if (IPython.notebook.kernel != null) {\n", + " IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n", + "}\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "flux = pcc.kcorr.calc_spectrum_filter_flux(filter_object=BessellB, spectrum_object=spec, \n", + " correct_for_area=True, verbose=True)\n", + "print(flux)\n", + "BessellB.plot()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "It looks like going back to a longer spectrum after a cropped and resampled one causes problems. If I run the `calc_spectrum_filter_flux` with a reloaded filter every time it might give me different results." + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "0.0681981953533 0.0681502713684\n", + "0.0703546166221 0.0701954395629\n", + "0.0952230850925 0.0965469897738\n", + "0.107621350594 0.107529497841\n", + "0.119768136655 0.120320638291\n", + "0.128729725263 0.121050105658\n", + "0.132208011408 0.125692565403\n", + "0.133922294034 0.118096168107\n", + "0.129547936621 0.119260622462\n", + "0.130204294446 0.129933844101\n", + "0.114518764848 0.105089299754\n", + "0.106609304644 0.0933475489263\n", + "0.0958183495558 0.0849714776482\n", + "0.0912305712487 0.072058782156\n", + "0.0792164587547 0.0709007368105\n", + "0.0638949428945 0.0499113387599\n", + "0.0610673471322 0.0370521507522\n", + "0.0539330243157 0.030758882816\n", + "0.0504622641925 0.0408396520279\n" + ] + } + ], + "source": [ + "sim_spec_flux_from_object = []\n", + "sim_spec_flux = []\n", + "sim_mjd_obs = []\n", + "\n", + "for spec in sn.sim_spec:\n", + "# print(spec)\n", + " flux = pcc.kcorr.calc_spectrum_filter_flux(filter_name=\"BessellB\", spectrum_object=sn.sim_spec[spec], \n", + " correct_for_area=True, verbose=False)\n", + " flux_from_object = pcc.kcorr.calc_spectrum_filter_flux(filter_object=BessellB, spectrum_object=sn.sim_spec[spec], \n", + " correct_for_area=True, verbose=False)\n", + " print(flux, flux_from_object)\n", + " mjd_obs = float(spec.split(\"_\")[-1])\n", + " \n", + " sim_spec_flux.append(flux)\n", + " sim_spec_flux_from_object.append(flux_from_object)\n", + " \n", + " sim_mjd_obs.append(mjd_obs)" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "application/javascript": [ + "/* Put everything inside the global mpl namespace */\n", + "window.mpl = {};\n", + "\n", + "\n", + "mpl.get_websocket_type = function() {\n", + " if (typeof(WebSocket) !== 'undefined') {\n", + " return WebSocket;\n", + " } else if (typeof(MozWebSocket) !== 'undefined') {\n", + " return MozWebSocket;\n", + " } else {\n", + " alert('Your browser does not have WebSocket support.' +\n", + " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", + " 'Firefox 4 and 5 are also supported but you ' +\n", + " 'have to enable WebSockets in about:config.');\n", + " };\n", + "}\n", + "\n", + "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", + " this.id = figure_id;\n", + "\n", + " this.ws = websocket;\n", + "\n", + " this.supports_binary = (this.ws.binaryType != undefined);\n", + "\n", + " if (!this.supports_binary) {\n", + " var warnings = document.getElementById(\"mpl-warnings\");\n", + " if (warnings) {\n", + " warnings.style.display = 'block';\n", + " warnings.textContent = (\n", + " \"This browser does not support binary websocket messages. \" +\n", + " \"Performance may be slow.\");\n", + " }\n", + " }\n", + "\n", + " this.imageObj = new Image();\n", + "\n", + " this.context = undefined;\n", + " this.message = undefined;\n", + " this.canvas = undefined;\n", + " this.rubberband_canvas = undefined;\n", + " this.rubberband_context = undefined;\n", + " this.format_dropdown = undefined;\n", + "\n", + " this.image_mode = 'full';\n", + "\n", + " this.root = $('
');\n", + " this._root_extra_style(this.root)\n", + " this.root.attr('style', 'display: inline-block');\n", + "\n", + " $(parent_element).append(this.root);\n", + "\n", + " this._init_header(this);\n", + " this._init_canvas(this);\n", + " this._init_toolbar(this);\n", + "\n", + " var fig = this;\n", + "\n", + " this.waiting = false;\n", + "\n", + " this.ws.onopen = function () {\n", + " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", + " fig.send_message(\"send_image_mode\", {});\n", + " if (mpl.ratio != 1) {\n", + " fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n", + " }\n", + " fig.send_message(\"refresh\", {});\n", + " }\n", + "\n", + " this.imageObj.onload = function() {\n", + " if (fig.image_mode == 'full') {\n", + " // Full images could contain transparency (where diff images\n", + " // almost always do), so we need to clear the canvas so that\n", + " // there is no ghosting.\n", + " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", + " }\n", + " fig.context.drawImage(fig.imageObj, 0, 0);\n", + " };\n", + "\n", + " this.imageObj.onunload = function() {\n", + " fig.ws.close();\n", + " }\n", + "\n", + " this.ws.onmessage = this._make_on_message_function(this);\n", + "\n", + " this.ondownload = ondownload;\n", + "}\n", + "\n", + "mpl.figure.prototype._init_header = function() {\n", + " var titlebar = $(\n", + " '
');\n", + " var titletext = $(\n", + " '
');\n", + " titlebar.append(titletext)\n", + " this.root.append(titlebar);\n", + " this.header = titletext[0];\n", + "}\n", + "\n", + "\n", + "\n", + "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", + "\n", + "}\n", + "\n", + "\n", + "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", + "\n", + "}\n", + "\n", + "mpl.figure.prototype._init_canvas = function() {\n", + " var fig = this;\n", + "\n", + " var canvas_div = $('
');\n", + "\n", + " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", + "\n", + " function canvas_keyboard_event(event) {\n", + " return fig.key_event(event, event['data']);\n", + " }\n", + "\n", + " canvas_div.keydown('key_press', canvas_keyboard_event);\n", + " canvas_div.keyup('key_release', canvas_keyboard_event);\n", + " this.canvas_div = canvas_div\n", + " this._canvas_extra_style(canvas_div)\n", + " this.root.append(canvas_div);\n", + "\n", + " var canvas = $('');\n", + " canvas.addClass('mpl-canvas');\n", + " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", + "\n", + " this.canvas = canvas[0];\n", + " this.context = canvas[0].getContext(\"2d\");\n", + "\n", + " var backingStore = this.context.backingStorePixelRatio ||\n", + "\tthis.context.webkitBackingStorePixelRatio ||\n", + "\tthis.context.mozBackingStorePixelRatio ||\n", + "\tthis.context.msBackingStorePixelRatio ||\n", + "\tthis.context.oBackingStorePixelRatio ||\n", + "\tthis.context.backingStorePixelRatio || 1;\n", + "\n", + " mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n", + "\n", + " var rubberband = $('');\n", + " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", + "\n", + " var pass_mouse_events = true;\n", + "\n", + " canvas_div.resizable({\n", + " start: function(event, ui) {\n", + " pass_mouse_events = false;\n", + " },\n", + " resize: function(event, ui) {\n", + " fig.request_resize(ui.size.width, ui.size.height);\n", + " },\n", + " stop: function(event, ui) {\n", + " pass_mouse_events = true;\n", + " fig.request_resize(ui.size.width, ui.size.height);\n", + " },\n", + " });\n", + "\n", + " function mouse_event_fn(event) {\n", + " if (pass_mouse_events)\n", + " return fig.mouse_event(event, event['data']);\n", + " }\n", + "\n", + " rubberband.mousedown('button_press', mouse_event_fn);\n", + " rubberband.mouseup('button_release', mouse_event_fn);\n", + " // Throttle sequential mouse events to 1 every 20ms.\n", + " rubberband.mousemove('motion_notify', mouse_event_fn);\n", + "\n", + " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", + " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", + "\n", + " canvas_div.on(\"wheel\", function (event) {\n", + " event = event.originalEvent;\n", + " event['data'] = 'scroll'\n", + " if (event.deltaY < 0) {\n", + " event.step = 1;\n", + " } else {\n", + " event.step = -1;\n", + " }\n", + " mouse_event_fn(event);\n", + " });\n", + "\n", + " canvas_div.append(canvas);\n", + " canvas_div.append(rubberband);\n", + "\n", + " this.rubberband = rubberband;\n", + " this.rubberband_canvas = rubberband[0];\n", + " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", + " this.rubberband_context.strokeStyle = \"#000000\";\n", + "\n", + " this._resize_canvas = function(width, height) {\n", + " // Keep the size of the canvas, canvas container, and rubber band\n", + " // canvas in synch.\n", + " canvas_div.css('width', width)\n", + " canvas_div.css('height', height)\n", + "\n", + " canvas.attr('width', width * mpl.ratio);\n", + " canvas.attr('height', height * mpl.ratio);\n", + " canvas.attr('style', 'width: ' + width + 'px; height: ' + height + 'px;');\n", + "\n", + " rubberband.attr('width', width);\n", + " rubberband.attr('height', height);\n", + " }\n", + "\n", + " // Set the figure to an initial 600x600px, this will subsequently be updated\n", + " // upon first draw.\n", + " this._resize_canvas(600, 600);\n", + "\n", + " // Disable right mouse context menu.\n", + " $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n", + " return false;\n", + " });\n", + "\n", + " function set_focus () {\n", + " canvas.focus();\n", + " canvas_div.focus();\n", + " }\n", + "\n", + " window.setTimeout(set_focus, 100);\n", + "}\n", + "\n", + "mpl.figure.prototype._init_toolbar = function() {\n", + " var fig = this;\n", + "\n", + " var nav_element = $('
')\n", + " nav_element.attr('style', 'width: 100%');\n", + " this.root.append(nav_element);\n", + "\n", + " // Define a callback function for later on.\n", + " function toolbar_event(event) {\n", + " return fig.toolbar_button_onclick(event['data']);\n", + " }\n", + " function toolbar_mouse_event(event) {\n", + " return fig.toolbar_button_onmouseover(event['data']);\n", + " }\n", + "\n", + " for(var toolbar_ind in mpl.toolbar_items) {\n", + " var name = mpl.toolbar_items[toolbar_ind][0];\n", + " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", + " var image = mpl.toolbar_items[toolbar_ind][2];\n", + " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", + "\n", + " if (!name) {\n", + " // put a spacer in here.\n", + " continue;\n", + " }\n", + " var button = $('');\n", + " button.click(method_name, toolbar_event);\n", + " button.mouseover(tooltip, toolbar_mouse_event);\n", + " nav_element.append(button);\n", + " }\n", + "\n", + " // Add the status bar.\n", + " var status_bar = $('');\n", + " nav_element.append(status_bar);\n", + " this.message = status_bar[0];\n", + "\n", + " // Add the close button to the window.\n", + " var buttongrp = $('
');\n", + " var button = $('');\n", + " button.click(function (evt) { fig.handle_close(fig, {}); } );\n", + " button.mouseover('Stop Interaction', toolbar_mouse_event);\n", + " buttongrp.append(button);\n", + " var titlebar = this.root.find($('.ui-dialog-titlebar'));\n", + " titlebar.prepend(buttongrp);\n", + "}\n", + "\n", + "mpl.figure.prototype._root_extra_style = function(el){\n", + " var fig = this\n", + " el.on(\"remove\", function(){\n", + "\tfig.close_ws(fig, {});\n", + " });\n", + "}\n", + "\n", + "mpl.figure.prototype._canvas_extra_style = function(el){\n", + " // this is important to make the div 'focusable\n", + " el.attr('tabindex', 0)\n", + " // reach out to IPython and tell the keyboard manager to turn it's self\n", + " // off when our div gets focus\n", + "\n", + " // location in version 3\n", + " if (IPython.notebook.keyboard_manager) {\n", + " IPython.notebook.keyboard_manager.register_events(el);\n", + " }\n", + " else {\n", + " // location in version 2\n", + " IPython.keyboard_manager.register_events(el);\n", + " }\n", + "\n", + "}\n", + "\n", + "mpl.figure.prototype._key_event_extra = function(event, name) {\n", + " var manager = IPython.notebook.keyboard_manager;\n", + " if (!manager)\n", + " manager = IPython.keyboard_manager;\n", + "\n", + " // Check for shift+enter\n", + " if (event.shiftKey && event.which == 13) {\n", + " this.canvas_div.blur();\n", + " event.shiftKey = false;\n", + " // Send a \"J\" for go to next cell\n", + " event.which = 74;\n", + " event.keyCode = 74;\n", + " manager.command_mode();\n", + " manager.handle_keydown(event);\n", + " }\n", + "}\n", + "\n", + "mpl.figure.prototype.handle_save = function(fig, msg) {\n", + " fig.ondownload(fig, null);\n", + "}\n", + "\n", + "\n", + "mpl.find_output_cell = function(html_output) {\n", + " // Return the cell and output element which can be found *uniquely* in the notebook.\n", + " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", + " // IPython event is triggered only after the cells have been serialised, which for\n", + " // our purposes (turning an active figure into a static one), is too late.\n", + " var cells = IPython.notebook.get_cells();\n", + " var ncells = cells.length;\n", + " for (var i=0; i= 3 moved mimebundle to data attribute of output\n", + " data = data.data;\n", + " }\n", + " if (data['text/html'] == html_output) {\n", + " return [cell, data, j];\n", + " }\n", + " }\n", + " }\n", + " }\n", + "}\n", + "\n", + "// Register the function which deals with the matplotlib target/channel.\n", + "// The kernel may be null if the page has been refreshed.\n", + "if (IPython.notebook.kernel != null) {\n", + " IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n", + "}\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "fig = plt.figure()\n", + "ax = fig.add_subplot(111)\n", + "ax.scatter(sim_mjd_obs, sim_spec_flux)\n", + "ax.scatter(sim_mjd_obs, sim_spec_flux_with_revert)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "ok, that's figured out, I'm going to insert a self.revert into the resample by default." + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "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": "3.6.0" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/notebooks/Tutorials/1 - pycoco calling CoCo.ipynb b/notebooks/Tutorials/1 - pycoco calling CoCo.ipynb index a190d59..ac6d6de 100644 --- a/notebooks/Tutorials/1 - pycoco calling CoCo.ipynb +++ b/notebooks/Tutorials/1 - pycoco calling CoCo.ipynb @@ -16,7 +16,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -49,17 +49,9 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 2, "metadata": {}, "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/berto/anaconda3/envs/pycoco/lib/python3.6/site-packages/pycoco/utils.py:213: UserWarning: /Users/berto/Code/verbose-enigma/notebooks/Tutorials/SN2006aj is not a valid file. Returning 'False'.\n", - " \" is not a valid file. Returning 'False'.\")\n" - ] - }, { "name": "stdout", "output_type": "stream", @@ -70,6 +62,14 @@ "callargs are ['/Users/berto/Code/CoCo/lcfit', 'SN2006aj']\n", "Fit complete\n" ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/Users/berto/anaconda3/lib/python3.6/site-packages/pycocosn-0.9.14-py3.6.egg/pycoco/utils.py:216: UserWarning: /Users/berto/Code/verbose-enigma/notebooks/Tutorials/SN2006aj is not a valid file. Returning 'False'.\n", + " \" is not a valid file. Returning 'False'.\")\n" + ] } ], "source": [ @@ -95,8 +95,8 @@ "text": [ "current list.txt is up to date. re run with force = True to force.\n", "No Model supplied - running with default\n", - "Running CoCo lcfit on /Users/berto/Code/CoCo/data/lc/SN2006aj.dat\n", - "callargs are ['/Users/berto/Code/CoCo/lcfit', '/Users/berto/Code/CoCo/data/lc/SN2006aj.dat']\n", + "Running CoCo lcfit on /Users/berto/Code/CoCo//data/lc/SN2006aj.dat\n", + "callargs are ['/Users/berto/Code/CoCo/lcfit', '/Users/berto/Code/CoCo//data/lc/SN2006aj.dat']\n", "Fit complete\n" ] } @@ -669,7 +669,7 @@ "};\n", "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Pan axes with left mouse, zoom with right\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n", "\n", - "mpl.extensions = [\"eps\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\"];\n", + "mpl.extensions = [\"eps\", \"jpeg\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n", "\n", "mpl.default_extension = \"png\";var comm_websocket_adapter = function(comm) {\n", " // Create a \"websocket\"-like object which calls the given IPython comm\n", @@ -893,7 +893,7 @@ { "data": { "text/html": [ - "" + "" ], "text/plain": [ "" @@ -913,28 +913,214 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "pcc.coco.run_LCfit(os.path.join(pcc.defaults._default_data_dir_path, \"lc/\"+snname+\".dat\"), model=\"Karpenka12\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "sn = pcc.classes.SNClass(snname)\n", + "sn.load_phot(verbose=False)\n", + "sn.get_lcfit(os.path.join(pcc.defaults._default_recon_dir_path, snname + \".dat\"))\n", + "\n", + "sn.plot_lc(multiplot=False)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Model Choice\n", + "----\n", + "You can also pass a model to **`CoCo lcfit`**, this is possible through **`pycoco`** using the `model` arg. This will only take models that are defined in CoCo/src/models and match the filenames. So, currently the valid models are:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "models = np.unique([i.split(\".\")[0] for i in os.listdir(os.path.join(pcc.defaults._default_coco_dir_path, \"src/models\"))])\n", + "models" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "model_name = \"Karpenka12\"\n", + "# model_name = \"Karpenka12Afterglow\"\n", + "# model_name = \"Kessler10\"\n", + "pcc.coco.run_LCfit(os.path.join(pcc.defaults._default_data_dir_path, \"lc/\"+snname+\".dat\"), model=model_name, verbose=True)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "sn = pcc.classes.SNClass(snname)\n", + "sn.load_phot(verbose=False)\n", + "sn.get_lcfit(os.path.join(pcc.defaults._default_recon_dir_path, snname + \".dat\"))\n", + "\n", + "sn.plot_lc(multiplot=False)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## All SNe as Batch\n", + "___" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": false + }, + "outputs": [], + "source": [ + "pcc.coco.run_LCfit_fileinput(os.path.join(pcc.defaults._default_coco_dir_path, \"examples/lc.list\"))\n", + "print(\"Done.\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Call Specfit\n", + "---\n", + "\n", + "### individual speclists" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "pcc.coco.get_all_spec_lists()" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "sn.load_list(path=os.path.join(pcc.defaults._default_list_dir_path, sn.name+\".list\"))\n", + "sn.load_spec()\n", + "\n", + "# sn.load_mangledspec()\n", + "sn.load_reconspec()\n", + "sn.load_simspec()\n" + ] + }, + { + "cell_type": "code", + "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "current list.txt is up to date. re run with force = True to force.\n", - "running with Karpenka12\n", - "Running CoCo lcfit on /Users/berto/Code/CoCo/data/lc/SN2006aj.dat\n", - "callargs are ['/Users/berto/Code/CoCo/lcfit', '/Users/berto/Code/CoCo/data/lc/SN2006aj.dat', '-m', 'Karpenka12']\n", - "Fit complete\n" + "SN2006aj_53786.270000\n", + "Filter_area = 958.904702526\n", + "Integrated flux = 65.3955702281\n", + "SN2006aj_53787.230000\n", + "Filter_area = 583.185950131\n", + "Integrated flux = 41.0298233406\n", + "SN2006aj_53788.200000\n", + "Filter_area = 1358.72907164\n", + "Integrated flux = 131.886385781\n", + "SN2006aj_53789.170000\n", + "Filter_area = 1357.72217486\n", + "Integrated flux = 146.521717503\n", + "SN2006aj_53790.140000\n", + "Filter_area = 1361.80653493\n", + "Integrated flux = 164.34213622\n", + "SN2006aj_53791.100000\n", + "Filter_area = 1356.94789874\n", + "Integrated flux = 163.802182486\n", + "SN2006aj_53792.070000\n", + "Filter_area = 1358.08475139\n", + "Integrated flux = 170.17603978\n", + "SN2006aj_53793.040000\n", + "Filter_area = 1342.63870674\n", + "Integrated flux = 156.866851118\n", + "SN2006aj_53794.010000\n", + "Filter_area = 1358.55873129\n", + "Integrated flux = 160.605022385\n", + "SN2006aj_53794.970000\n", + "Filter_area = 494.406955809\n", + "Integrated flux = 64.3739416067\n", + "SN2006aj_53795.940000\n", + "Filter_area = 1315.20012487\n", + "Integrated flux = 137.109302356\n", + "SN2006aj_53796.910000\n", + "Filter_area = 1313.60589901\n", + "Integrated flux = 121.107583058\n", + "SN2006aj_53797.880000\n", + "Filter_area = 1313.47758368\n", + "Integrated flux = 110.196456176\n", + "SN2006aj_53798.840000\n", + "Filter_area = 1315.40072684\n", + "Integrated flux = 92.2847571523\n", + "SN2006aj_53799.810000\n", + "Filter_area = 1314.80756892\n", + "Integrated flux = 91.8528874753\n", + "SN2006aj_53801.750000\n", + "Filter_area = 1298.16443106\n", + "Integrated flux = 63.0384962734\n", + "SN2006aj_53802.720000\n", + "Filter_area = 1299.82908919\n", + "Integrated flux = 45.3544694847\n", + "SN2006aj_53803.680000\n", + "Filter_area = 1296.91402526\n", + "Integrated flux = 37.1949955268\n", + "SN2006aj_53803.680001\n", + "Filter_area = 1296.93821395\n", + "Integrated flux = 51.5059756933\n" ] } ], "source": [ - "pcc.coco.run_LCfit(os.path.join(pcc.defaults._default_data_dir_path, \"lc/\"+snname+\".dat\"), model=\"Karpenka12\")" + "path_to_filter = os.path.join(pcc.defaults._default_filter_dir_path,\"BessellB.dat\")\n", + "BessellB = pcc.classes.FilterClass()\n", + "BessellB.read_filter_file(path_to_filter)\n", + "BessellB.calculate_AB_zp()\n", + "\n", + "sim_spec_flux = []\n", + "sim_mjd_obs = []\n", + "\n", + "for spec in sn.sim_spec:\n", + " print(spec)\n", + " flux = pcc.kcorr.calc_spectrum_filter_flux(filter_object=BessellB, spectrum_object=sn.sim_spec[spec], \n", + " correct_for_area=False)\n", + " mjd_obs = float(spec.split(\"_\")[-1])\n", + " \n", + " sim_spec_flux.append(flux)\n", + " sim_mjd_obs.append(mjd_obs)" ] }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 11, "metadata": {}, "outputs": [ { @@ -1496,7 +1682,7 @@ "};\n", "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Pan axes with left mouse, zoom with right\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n", "\n", - "mpl.extensions = [\"eps\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\"];\n", + "mpl.extensions = [\"eps\", \"jpeg\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n", "\n", "mpl.default_extension = \"png\";var comm_websocket_adapter = function(comm) {\n", " // Create a \"websocket\"-like object which calls the given IPython comm\n", @@ -1720,7 +1906,7 @@ { "data": { "text/html": [ - "" + "" ], "text/plain": [ "" @@ -1728,935 +1914,31 @@ }, "metadata": {}, "output_type": "display_data" - } - ], - "source": [ - "sn = pcc.classes.SNClass(snname)\n", - "sn.load_phot(verbose=False)\n", - "sn.get_lcfit(os.path.join(pcc.defaults._default_recon_dir_path, snname + \".dat\"))\n", - "\n", - "sn.plot_lc(multiplot=False)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Model Choice\n", - "----\n", - "You can also pass a model to **`CoCo lcfit`**, this is possible through **`pycoco`** using the `model` arg. This will only take models that are defined in CoCo/src/models and match the filenames. So, currently the valid models are:" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [ + }, { "data": { "text/plain": [ - "array(['Bazin09', 'Firth17Complex', 'Karpenka12', 'Karpenka12Afterglow',\n", - " 'Kessler10', 'LinearMangle', 'SpecMangle'],\n", - " dtype='" ] }, - "execution_count": 9, + "execution_count": 11, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "models = np.unique([i.split(\".\")[0] for i in os.listdir(os.path.join(pcc.defaults._default_coco_dir_path, \"src/models\"))])\n", - "models" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "current list.txt is up to date. re run with force = True to force.\n", - "running with Karpenka12\n", - "Running CoCo lcfit on /Users/berto/Code/CoCo/data/lc/SN2006aj.dat\n", - "callargs are ['/Users/berto/Code/CoCo/lcfit', '/Users/berto/Code/CoCo/data/lc/SN2006aj.dat', '-m', 'Karpenka12']\n", - "Fit complete\n" - ] - } - ], - "source": [ - "model_name = \"Karpenka12\"\n", - "# model_name = \"Karpenka12Afterglow\"\n", - "# model_name = \"Kessler10\"\n", - "pcc.coco.run_LCfit(os.path.join(pcc.defaults._default_data_dir_path, \"lc/\"+snname+\".dat\"), model=model_name, verbose=True)" + "fig = plt.figure()\n", + "ax = fig.add_subplot(111)\n", + "ax.scatter(sim_mjd_obs, sim_spec_flux)\n" ] }, { "cell_type": "code", - "execution_count": 11, - "metadata": {}, - "outputs": [ - { - "data": { - "application/javascript": [ - "/* Put everything inside the global mpl namespace */\n", - "window.mpl = {};\n", - "\n", - "\n", - "mpl.get_websocket_type = function() {\n", - " if (typeof(WebSocket) !== 'undefined') {\n", - " return WebSocket;\n", - " } else if (typeof(MozWebSocket) !== 'undefined') {\n", - " return MozWebSocket;\n", - " } else {\n", - " alert('Your browser does not have WebSocket support.' +\n", - " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", - " 'Firefox 4 and 5 are also supported but you ' +\n", - " 'have to enable WebSockets in about:config.');\n", - " };\n", - "}\n", - "\n", - "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", - " this.id = figure_id;\n", - "\n", - " this.ws = websocket;\n", - "\n", - " this.supports_binary = (this.ws.binaryType != undefined);\n", - "\n", - " if (!this.supports_binary) {\n", - " var warnings = document.getElementById(\"mpl-warnings\");\n", - " if (warnings) {\n", - " warnings.style.display = 'block';\n", - " warnings.textContent = (\n", - " \"This browser does not support binary websocket messages. \" +\n", - " \"Performance may be slow.\");\n", - " }\n", - " }\n", - "\n", - " this.imageObj = new Image();\n", - "\n", - " this.context = undefined;\n", - " this.message = undefined;\n", - " this.canvas = undefined;\n", - " this.rubberband_canvas = undefined;\n", - " this.rubberband_context = undefined;\n", - " this.format_dropdown = undefined;\n", - "\n", - " this.image_mode = 'full';\n", - "\n", - " this.root = $('
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