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investigate_harmonize_env_param_time_failure.ipynb
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| { | |
| "cells": [ | |
| { | |
| "cell_type": "code", | |
| "execution_count": 1, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "# Import Packages\n", | |
| "import echopype as ep\n", | |
| "import xarray as xr" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "I started from the error and worked my way back to the merging of EK80 complex datasets.\n", | |
| "\n", | |
| "In Echopype Code I set print statements in `merge_save` function of `echopype/convert/set_groups_ek80.py`. This is to show where exactly I am capturing the output I will show below:\n", | |
| "```\n", | |
| "@staticmethod\n", | |
| "def merge_save(ds_combine: List[xr.Dataset], ds_invariant: xr.Dataset) -> xr.Dataset:\n", | |
| " \"\"\"Merge data from all complex or all power/angle channels\"\"\"\n", | |
| " # Combine all channels into one Dataset\n", | |
| " print(\"Transmit Frequency Channel 1 Pre Combine:\", ds_combine[0][\"transmit_frequency_start\"])\n", | |
| " print(\"Transmit Frequency Channel 1 Ping Time Pre Combine:\", ds_combine[0][\"transmit_frequency_start\"][\"ping_time\"])\n", | |
| " print(\"Transmit Frequency Channel 2 Pre Combine:\",ds_combine[1][\"transmit_frequency_start\"])\n", | |
| " print(\"Transmit Frequency Channel 2 Ping Time Pre Combine:\", ds_combine[1][\"transmit_frequency_start\"][\"ping_time\"])\n", | |
| " ds_combine = xr.concat(ds_combine, dim=\"channel\")\n", | |
| " print(\"Transmit Frequency Combined:\", ds_combine[\"transmit_frequency_start\"])\n", | |
| " ds_combine = xr.merge(\n", | |
| " [ds_invariant, ds_combine], combine_attrs=\"override\"\n", | |
| " ) # override keeps the Dataset attributes\n", | |
| " return set_time_encodings(ds_combine)\n", | |
| "```" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "The ping time values for both arrays are inconsistent with each other:\n", | |
| "\n", | |
| "(Also, note that these ping time values come from the `parser_obj` in `SetGroupsEK80`)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 2, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "Transmit Frequency Channel 1 Pre Combine: <xarray.DataArray 'transmit_frequency_start' (channel: 1, ping_time: 31)>\n", | |
| "array([[160000., 160000., 160000., 160000., 160000., 160000., 160000.,\n", | |
| " 160000., 160000., 160000., 160000., 160000., 160000., 160000.,\n", | |
| " 160000., 160000., 160000., 160000., 160000., 160000., 160000.,\n", | |
| " 160000., 160000., 160000., 160000., 160000., 160000., 160000.,\n", | |
| " 160000., 160000., 160000.]])\n", | |
| "Coordinates:\n", | |
| " * channel (channel) object 'WBT Mini 274021-15-1 ES200-7C_ES'\n", | |
| " * ping_time (ping_time) datetime64[ns] 2023-10-03T12:00:53.559627776 ... 2...\n", | |
| "Attributes:\n", | |
| " long_name: Start frequency in transmitted pulse\n", | |
| " units: Hz\n", | |
| " standard_name: sound_frequency\n", | |
| " valid_min: 0.0\n", | |
| "Transmit Frequency Channel 1 Ping Time Pre Combine: <xarray.DataArray 'ping_time' (ping_time: 31)>\n", | |
| "array(['2023-10-03T12:00:53.559627776', '2023-10-03T12:00:55.562006016',\n", | |
| " '2023-10-03T12:00:57.569653248', '2023-10-03T12:00:59.553221120',\n", | |
| " '2023-10-03T12:01:01.922873856', '2023-10-03T12:01:03.949699072',\n", | |
| " '2023-10-03T12:01:05.950732800', '2023-10-03T12:01:07.965466112',\n", | |
| " '2023-10-03T12:01:09.937934848', '2023-10-03T12:01:12.291490816',\n", | |
| " '2023-10-03T12:01:14.304367104', '2023-10-03T12:01:16.317727744',\n", | |
| " '2023-10-03T12:01:18.330081792', '2023-10-03T12:01:20.304416768',\n", | |
| " '2023-10-03T12:01:22.737865216', '2023-10-03T12:01:24.772293120',\n", | |
| " '2023-10-03T12:01:26.794712064', '2023-10-03T12:01:28.811527168',\n", | |
| " '2023-10-03T12:01:30.821850112', '2023-10-03T12:01:33.201689088',\n", | |
| " '2023-10-03T12:01:35.215869952', '2023-10-03T12:01:37.228828160',\n", | |
| " '2023-10-03T12:01:39.242184192', '2023-10-03T12:01:41.244993024',\n", | |
| " '2023-10-03T12:01:43.603165184', '2023-10-03T12:01:45.620483072',\n", | |
| " '2023-10-03T12:01:47.643970048', '2023-10-03T12:01:49.635296256',\n", | |
| " '2023-10-03T12:01:51.644869120', '2023-10-03T12:01:54.007105024',\n", | |
| " '2023-10-03T12:01:56.051064832'], dtype='datetime64[ns]')\n", | |
| "Coordinates:\n", | |
| " * ping_time (ping_time) datetime64[ns] 2023-10-03T12:00:53.559627776 ... 2...\n", | |
| "Attributes:\n", | |
| " long_name: Timestamp of each ping\n", | |
| " standard_name: time\n", | |
| " axis: T\n", | |
| "Transmit Frequency Channel 2 Pre Combine: <xarray.DataArray 'transmit_frequency_start' (channel: 1, ping_time: 32)>\n", | |
| "array([[55000., 55000., 55000., 55000., 55000., 55000., 55000., 55000.,\n", | |
| " 55000., 55000., 55000., 55000., 55000., 55000., 55000., 55000.,\n", | |
| " 55000., 55000., 55000., 55000., 55000., 55000., 55000., 55000.,\n", | |
| " 55000., 55000., 55000., 55000., 55000., 55000., 55000., 55000.]])\n", | |
| "Coordinates:\n", | |
| " * channel (channel) object 'WBT Mini 274021-15-2 ES70-18CD_ES'\n", | |
| " * ping_time (ping_time) datetime64[ns] 2023-10-03T12:00:51.976906240 ... 2...\n", | |
| "Attributes:\n", | |
| " long_name: Start frequency in transmitted pulse\n", | |
| " units: Hz\n", | |
| " standard_name: sound_frequency\n", | |
| " valid_min: 0.0\n", | |
| "Transmit Frequency Channel 2 Ping Time Pre Combine: <xarray.DataArray 'ping_time' (ping_time: 32)>\n", | |
| "array(['2023-10-03T12:00:51.976906240', '2023-10-03T12:00:54.005223936',\n", | |
| " '2023-10-03T12:00:56.009693184', '2023-10-03T12:00:57.993319936',\n", | |
| " '2023-10-03T12:01:00.363073024', '2023-10-03T12:01:02.371548160',\n", | |
| " '2023-10-03T12:01:04.401380864', '2023-10-03T12:01:06.407278080',\n", | |
| " '2023-10-03T12:01:08.388156928', '2023-10-03T12:01:10.748850176',\n", | |
| " '2023-10-03T12:01:12.745195008', '2023-10-03T12:01:14.748951040',\n", | |
| " '2023-10-03T12:01:16.772888064', '2023-10-03T12:01:18.751777792',\n", | |
| " '2023-10-03T12:01:21.177158144', '2023-10-03T12:01:23.196512256',\n", | |
| " '2023-10-03T12:01:25.233106944', '2023-10-03T12:01:27.250378240',\n", | |
| " '2023-10-03T12:01:29.245244928', '2023-10-03T12:01:31.646898176',\n", | |
| " '2023-10-03T12:01:33.640371200', '2023-10-03T12:01:35.653824000',\n", | |
| " '2023-10-03T12:01:37.674447872', '2023-10-03T12:01:39.659781120',\n", | |
| " '2023-10-03T12:01:42.054491136', '2023-10-03T12:01:44.049811968',\n", | |
| " '2023-10-03T12:01:46.073785856', '2023-10-03T12:01:48.087618048',\n", | |
| " '2023-10-03T12:01:50.058952192', '2023-10-03T12:01:52.455427072',\n", | |
| " '2023-10-03T12:01:54.474840064', '2023-10-03T12:01:56.517842944'],\n", | |
| " dtype='datetime64[ns]')\n", | |
| "Coordinates:\n", | |
| " * ping_time (ping_time) datetime64[ns] 2023-10-03T12:00:51.976906240 ... 2...\n", | |
| "Attributes:\n", | |
| " long_name: Timestamp of each ping\n", | |
| " standard_name: time\n", | |
| " axis: T\n", | |
| "Transmit Frequency Combined: <xarray.DataArray 'transmit_frequency_start' (channel: 2, ping_time: 63)>\n", | |
| "array([[ nan, 160000., nan, 160000., nan, 160000., nan,\n", | |
| " 160000., nan, 160000., nan, 160000., nan, 160000.,\n", | |
| " nan, 160000., nan, 160000., nan, 160000., nan,\n", | |
| " 160000., nan, 160000., nan, 160000., nan, 160000.,\n", | |
| " nan, 160000., nan, 160000., nan, 160000., nan,\n", | |
| " 160000., nan, 160000., nan, 160000., nan, 160000.,\n", | |
| " nan, 160000., nan, 160000., nan, 160000., nan,\n", | |
| " 160000., nan, 160000., nan, 160000., nan, 160000.,\n", | |
| " nan, 160000., nan, 160000., nan, 160000., nan],\n", | |
| " [ 55000., nan, 55000., nan, 55000., nan, 55000.,\n", | |
| " nan, 55000., nan, 55000., nan, 55000., nan,\n", | |
| " 55000., nan, 55000., nan, 55000., nan, 55000.,\n", | |
| " nan, 55000., nan, 55000., nan, 55000., nan,\n", | |
| " 55000., nan, 55000., nan, 55000., nan, 55000.,\n", | |
| " nan, 55000., nan, 55000., nan, 55000., nan,\n", | |
| " 55000., nan, 55000., nan, 55000., nan, 55000.,\n", | |
| " nan, 55000., nan, 55000., nan, 55000., nan,\n", | |
| " 55000., nan, 55000., nan, 55000., nan, 55000.]])\n", | |
| "Coordinates:\n", | |
| " * ping_time (ping_time) datetime64[ns] 2023-10-03T12:00:51.976906240 ... 2...\n", | |
| " * channel (channel) object 'WBT Mini 274021-15-1 ES200-7C_ES' 'WBT Mini ...\n", | |
| "Attributes:\n", | |
| " long_name: Start frequency in transmitted pulse\n", | |
| " units: Hz\n", | |
| " standard_name: sound_frequency\n", | |
| " valid_min: 0.0\n" | |
| ] | |
| }, | |
| { | |
| "name": "stderr", | |
| "output_type": "stream", | |
| "text": [ | |
| "/home/exouser/miniforge3/envs/echopype/lib/python3.9/site-packages/xarray/core/duck_array_ops.py:187: RuntimeWarning: invalid value encountered in cast\n", | |
| " return data.astype(dtype, **kwargs)\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "# Read Raw\n", | |
| "ed = ep.open_raw(\"DRIX08-D20231003-T120051.raw\", sonar_model=\"EK80\")" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "The inconsistent ping times in both channels prior to combining leads us to the alternating NaN pattern post combining." | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "Now why does this matter? Later on, when we calculate sound absorption, we use the `transmit_frequency_start` and `transmit_frequency_end` variables in elementwise operations, thus leaving us with the same alternating NaN values." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 3, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "sound_absorption_da = xr.open_dataset(\"sound_absorption.zarr\", engine=\"zarr\")" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
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| ".xr-array-preview {\n", | |
| " display: inline-block;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list {\n", | |
| " display: inline-block !important;\n", | |
| " list-style: none;\n", | |
| " padding: 0 !important;\n", | |
| " margin: 0;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list li {\n", | |
| " display: inline-block;\n", | |
| " padding: 0;\n", | |
| " margin: 0;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list:before {\n", | |
| " content: '(';\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list:after {\n", | |
| " content: ')';\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list li:not(:last-child):after {\n", | |
| " content: ',';\n", | |
| " padding-right: 5px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-has-index {\n", | |
| " font-weight: bold;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-list,\n", | |
| ".xr-var-item {\n", | |
| " display: contents;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-item > div,\n", | |
| ".xr-var-item label,\n", | |
| ".xr-var-item > .xr-var-name span {\n", | |
| " background-color: var(--xr-background-color-row-even);\n", | |
| " margin-bottom: 0;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-item > .xr-var-name:hover span {\n", | |
| " padding-right: 5px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-list > li:nth-child(odd) > div,\n", | |
| ".xr-var-list > li:nth-child(odd) > label,\n", | |
| ".xr-var-list > li:nth-child(odd) > .xr-var-name span {\n", | |
| " background-color: var(--xr-background-color-row-odd);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name {\n", | |
| " grid-column: 1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-dims {\n", | |
| " grid-column: 2;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-dtype {\n", | |
| " grid-column: 3;\n", | |
| " text-align: right;\n", | |
| " color: var(--xr-font-color2);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-preview {\n", | |
| " grid-column: 4;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-index-preview {\n", | |
| " grid-column: 2 / 5;\n", | |
| " color: var(--xr-font-color2);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name,\n", | |
| ".xr-var-dims,\n", | |
| ".xr-var-dtype,\n", | |
| ".xr-preview,\n", | |
| ".xr-attrs dt {\n", | |
| " white-space: nowrap;\n", | |
| " overflow: hidden;\n", | |
| " text-overflow: ellipsis;\n", | |
| " padding-right: 10px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name:hover,\n", | |
| ".xr-var-dims:hover,\n", | |
| ".xr-var-dtype:hover,\n", | |
| ".xr-attrs dt:hover {\n", | |
| " overflow: visible;\n", | |
| " width: auto;\n", | |
| " z-index: 1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-attrs,\n", | |
| ".xr-var-data,\n", | |
| ".xr-index-data {\n", | |
| " display: none;\n", | |
| " background-color: var(--xr-background-color) !important;\n", | |
| " padding-bottom: 5px !important;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n", | |
| ".xr-var-data-in:checked ~ .xr-var-data,\n", | |
| ".xr-index-data-in:checked ~ .xr-index-data {\n", | |
| " display: block;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-data > table {\n", | |
| " float: right;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name span,\n", | |
| ".xr-var-data,\n", | |
| ".xr-index-name div,\n", | |
| ".xr-index-data,\n", | |
| ".xr-attrs {\n", | |
| " padding-left: 25px !important;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs,\n", | |
| ".xr-var-attrs,\n", | |
| ".xr-var-data,\n", | |
| ".xr-index-data {\n", | |
| " grid-column: 1 / -1;\n", | |
| "}\n", | |
| "\n", | |
| "dl.xr-attrs {\n", | |
| " padding: 0;\n", | |
| " margin: 0;\n", | |
| " display: grid;\n", | |
| " grid-template-columns: 125px auto;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt,\n", | |
| ".xr-attrs dd {\n", | |
| " padding: 0;\n", | |
| " margin: 0;\n", | |
| " float: left;\n", | |
| " padding-right: 10px;\n", | |
| " width: auto;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt {\n", | |
| " font-weight: normal;\n", | |
| " grid-column: 1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt:hover span {\n", | |
| " display: inline-block;\n", | |
| " background: var(--xr-background-color);\n", | |
| " padding-right: 10px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dd {\n", | |
| " grid-column: 2;\n", | |
| " white-space: pre-wrap;\n", | |
| " word-break: break-all;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-icon-database,\n", | |
| ".xr-icon-file-text2,\n", | |
| ".xr-no-icon {\n", | |
| " display: inline-block;\n", | |
| " vertical-align: middle;\n", | |
| " width: 1em;\n", | |
| " height: 1.5em !important;\n", | |
| " stroke-width: 0;\n", | |
| " stroke: currentColor;\n", | |
| " fill: currentColor;\n", | |
| "}\n", | |
| "</style><pre class='xr-text-repr-fallback'><xarray.DataArray 'sound_absorption' (time1: 1, channel: 2, ping_time: 63)>\n", | |
| "array([[[ nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan],\n", | |
| " [0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539]]])\n", | |
| "Coordinates:\n", | |
| " * channel (channel) <U33 'WBT Mini 274021-15-1 ES200-7C_ES' 'WBT Mini 27...\n", | |
| " * ping_time (ping_time) datetime64[ns] 2023-10-03T12:00:51.976906240 ... 2...\n", | |
| " * time1 (time1) datetime64[ns] 2023-10-03T12:00:51.976906240</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'sound_absorption'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>time1</span>: 1</li><li><span class='xr-has-index'>channel</span>: 2</li><li><span class='xr-has-index'>ping_time</span>: 63</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-827fc27c-1199-460b-b4ad-a54efe739070' class='xr-array-in' type='checkbox' checked><label for='section-827fc27c-1199-460b-b4ad-a54efe739070' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>nan 0.05424 nan 0.05424 nan ... 0.02357 nan 0.02357 nan 0.02357</span></div><div class='xr-array-data'><pre>array([[[ nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan],\n", | |
| " [0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539]]])</pre></div></div></li><li class='xr-section-item'><input id='section-111875e0-9142-4aad-8496-228d305bbb07' class='xr-section-summary-in' type='checkbox' checked><label for='section-111875e0-9142-4aad-8496-228d305bbb07' class='xr-section-summary' >Coordinates: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>channel</span></div><div class='xr-var-dims'>(channel)</div><div class='xr-var-dtype'><U33</div><div class='xr-var-preview xr-preview'>'WBT Mini 274021-15-1 ES200-7C_E...</div><input id='attrs-0de4b3df-5edb-4342-abc0-1153f7c66b35' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-0de4b3df-5edb-4342-abc0-1153f7c66b35' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c3414cde-199b-4b96-ba76-33ddcb367470' class='xr-var-data-in' type='checkbox'><label for='data-c3414cde-199b-4b96-ba76-33ddcb367470' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Vendor channel ID</dd></dl></div><div class='xr-var-data'><pre>array(['WBT Mini 274021-15-1 ES200-7C_ES', 'WBT Mini 274021-15-2 ES70-18CD_ES'],\n", | |
| " dtype='<U33')</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>ping_time</span></div><div class='xr-var-dims'>(ping_time)</div><div class='xr-var-dtype'>datetime64[ns]</div><div class='xr-var-preview xr-preview'>2023-10-03T12:00:51.976906240 .....</div><input id='attrs-707e9c6c-176b-47ed-9bff-166f5f6703f6' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-707e9c6c-176b-47ed-9bff-166f5f6703f6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6404ec14-e517-46ce-9709-9bd200cbee73' class='xr-var-data-in' type='checkbox'><label for='data-6404ec14-e517-46ce-9709-9bd200cbee73' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>axis :</span></dt><dd>T</dd><dt><span>long_name :</span></dt><dd>Timestamp of each ping</dd><dt><span>standard_name :</span></dt><dd>time</dd></dl></div><div class='xr-var-data'><pre>array(['2023-10-03T12:00:51.976906240', '2023-10-03T12:00:53.559627776',\n", | |
| " '2023-10-03T12:00:54.005223936', '2023-10-03T12:00:55.562006016',\n", | |
| " '2023-10-03T12:00:56.009693184', '2023-10-03T12:00:57.569653248',\n", | |
| " '2023-10-03T12:00:57.993319936', '2023-10-03T12:00:59.553221120',\n", | |
| " '2023-10-03T12:01:00.363073024', '2023-10-03T12:01:01.922873856',\n", | |
| " '2023-10-03T12:01:02.371548160', '2023-10-03T12:01:03.949699072',\n", | |
| " '2023-10-03T12:01:04.401380864', '2023-10-03T12:01:05.950732800',\n", | |
| " '2023-10-03T12:01:06.407278080', '2023-10-03T12:01:07.965466112',\n", | |
| " '2023-10-03T12:01:08.388156928', '2023-10-03T12:01:09.937934848',\n", | |
| " '2023-10-03T12:01:10.748850176', '2023-10-03T12:01:12.291490816',\n", | |
| " '2023-10-03T12:01:12.745195008', '2023-10-03T12:01:14.304367104',\n", | |
| " '2023-10-03T12:01:14.748951040', '2023-10-03T12:01:16.317727744',\n", | |
| " '2023-10-03T12:01:16.772888064', '2023-10-03T12:01:18.330081792',\n", | |
| " '2023-10-03T12:01:18.751777792', '2023-10-03T12:01:20.304416768',\n", | |
| " '2023-10-03T12:01:21.177158144', '2023-10-03T12:01:22.737865216',\n", | |
| " '2023-10-03T12:01:23.196512256', '2023-10-03T12:01:24.772293120',\n", | |
| " '2023-10-03T12:01:25.233106944', '2023-10-03T12:01:26.794712064',\n", | |
| " '2023-10-03T12:01:27.250378240', '2023-10-03T12:01:28.811527168',\n", | |
| " '2023-10-03T12:01:29.245244928', '2023-10-03T12:01:30.821850112',\n", | |
| " '2023-10-03T12:01:31.646898176', '2023-10-03T12:01:33.201689088',\n", | |
| " '2023-10-03T12:01:33.640371200', '2023-10-03T12:01:35.215869952',\n", | |
| " '2023-10-03T12:01:35.653824000', '2023-10-03T12:01:37.228828160',\n", | |
| " '2023-10-03T12:01:37.674447872', '2023-10-03T12:01:39.242184192',\n", | |
| " '2023-10-03T12:01:39.659781120', '2023-10-03T12:01:41.244993024',\n", | |
| " '2023-10-03T12:01:42.054491136', '2023-10-03T12:01:43.603165184',\n", | |
| " '2023-10-03T12:01:44.049811968', '2023-10-03T12:01:45.620483072',\n", | |
| " '2023-10-03T12:01:46.073785856', '2023-10-03T12:01:47.643970048',\n", | |
| " '2023-10-03T12:01:48.087618048', '2023-10-03T12:01:49.635296256',\n", | |
| " '2023-10-03T12:01:50.058952192', '2023-10-03T12:01:51.644869120',\n", | |
| " '2023-10-03T12:01:52.455427072', '2023-10-03T12:01:54.007105024',\n", | |
| " '2023-10-03T12:01:54.474840064', '2023-10-03T12:01:56.051064832',\n", | |
| " '2023-10-03T12:01:56.517842944'], dtype='datetime64[ns]')</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>time1</span></div><div class='xr-var-dims'>(time1)</div><div class='xr-var-dtype'>datetime64[ns]</div><div class='xr-var-preview xr-preview'>2023-10-03T12:00:51.976906240</div><input id='attrs-c3f6b524-7d8b-49ad-b14c-eac0caa550a8' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c3f6b524-7d8b-49ad-b14c-eac0caa550a8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3b38d8d7-7475-4fd9-ab81-6c08e2fa5cf0' class='xr-var-data-in' type='checkbox'><label for='data-3b38d8d7-7475-4fd9-ab81-6c08e2fa5cf0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>axis :</span></dt><dd>T</dd><dt><span>comment :</span></dt><dd>Time coordinate corresponding to environmental variables. Note that Platform.time3 is the same as Environment.time1.</dd><dt><span>long_name :</span></dt><dd>Timestamps for NMEA position datagrams</dd><dt><span>standard_name :</span></dt><dd>time</dd></dl></div><div class='xr-var-data'><pre>array(['2023-10-03T12:00:51.976906240'], dtype='datetime64[ns]')</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-a7db52e0-3c83-40dc-b161-a582ca40ebfd' class='xr-section-summary-in' type='checkbox' ><label for='section-a7db52e0-3c83-40dc-b161-a582ca40ebfd' class='xr-section-summary' >Indexes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>channel</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-5ebe2d0d-ee81-4c41-8ec2-eb1735a0b645' class='xr-index-data-in' type='checkbox'/><label for='index-5ebe2d0d-ee81-4c41-8ec2-eb1735a0b645' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index(['WBT Mini 274021-15-1 ES200-7C_ES', 'WBT Mini 274021-15-2 ES70-18CD_ES'], dtype='object', name='channel'))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>ping_time</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-73bdc4af-1894-406e-a16f-c6e2ec7da8e2' class='xr-index-data-in' type='checkbox'/><label for='index-73bdc4af-1894-406e-a16f-c6e2ec7da8e2' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(DatetimeIndex(['2023-10-03 12:00:51.976906240',\n", | |
| " '2023-10-03 12:00:53.559627776',\n", | |
| " '2023-10-03 12:00:54.005223936',\n", | |
| " '2023-10-03 12:00:55.562006016',\n", | |
| " '2023-10-03 12:00:56.009693184',\n", | |
| " '2023-10-03 12:00:57.569653248',\n", | |
| " '2023-10-03 12:00:57.993319936',\n", | |
| " '2023-10-03 12:00:59.553221120',\n", | |
| " '2023-10-03 12:01:00.363073024',\n", | |
| " '2023-10-03 12:01:01.922873856',\n", | |
| " '2023-10-03 12:01:02.371548160',\n", | |
| " '2023-10-03 12:01:03.949699072',\n", | |
| " '2023-10-03 12:01:04.401380864',\n", | |
| " '2023-10-03 12:01:05.950732800',\n", | |
| " '2023-10-03 12:01:06.407278080',\n", | |
| " '2023-10-03 12:01:07.965466112',\n", | |
| " '2023-10-03 12:01:08.388156928',\n", | |
| " '2023-10-03 12:01:09.937934848',\n", | |
| " '2023-10-03 12:01:10.748850176',\n", | |
| " '2023-10-03 12:01:12.291490816',\n", | |
| " '2023-10-03 12:01:12.745195008',\n", | |
| " '2023-10-03 12:01:14.304367104',\n", | |
| " '2023-10-03 12:01:14.748951040',\n", | |
| " '2023-10-03 12:01:16.317727744',\n", | |
| " '2023-10-03 12:01:16.772888064',\n", | |
| " '2023-10-03 12:01:18.330081792',\n", | |
| " '2023-10-03 12:01:18.751777792',\n", | |
| " '2023-10-03 12:01:20.304416768',\n", | |
| " '2023-10-03 12:01:21.177158144',\n", | |
| " '2023-10-03 12:01:22.737865216',\n", | |
| " '2023-10-03 12:01:23.196512256',\n", | |
| " '2023-10-03 12:01:24.772293120',\n", | |
| " '2023-10-03 12:01:25.233106944',\n", | |
| " '2023-10-03 12:01:26.794712064',\n", | |
| " '2023-10-03 12:01:27.250378240',\n", | |
| " '2023-10-03 12:01:28.811527168',\n", | |
| " '2023-10-03 12:01:29.245244928',\n", | |
| " '2023-10-03 12:01:30.821850112',\n", | |
| " '2023-10-03 12:01:31.646898176',\n", | |
| " '2023-10-03 12:01:33.201689088',\n", | |
| " '2023-10-03 12:01:33.640371200',\n", | |
| " '2023-10-03 12:01:35.215869952',\n", | |
| " '2023-10-03 12:01:35.653824',\n", | |
| " '2023-10-03 12:01:37.228828160',\n", | |
| " '2023-10-03 12:01:37.674447872',\n", | |
| " '2023-10-03 12:01:39.242184192',\n", | |
| " '2023-10-03 12:01:39.659781120',\n", | |
| " '2023-10-03 12:01:41.244993024',\n", | |
| " '2023-10-03 12:01:42.054491136',\n", | |
| " '2023-10-03 12:01:43.603165184',\n", | |
| " '2023-10-03 12:01:44.049811968',\n", | |
| " '2023-10-03 12:01:45.620483072',\n", | |
| " '2023-10-03 12:01:46.073785856',\n", | |
| " '2023-10-03 12:01:47.643970048',\n", | |
| " '2023-10-03 12:01:48.087618048',\n", | |
| " '2023-10-03 12:01:49.635296256',\n", | |
| " '2023-10-03 12:01:50.058952192',\n", | |
| " '2023-10-03 12:01:51.644869120',\n", | |
| " '2023-10-03 12:01:52.455427072',\n", | |
| " '2023-10-03 12:01:54.007105024',\n", | |
| " '2023-10-03 12:01:54.474840064',\n", | |
| " '2023-10-03 12:01:56.051064832',\n", | |
| " '2023-10-03 12:01:56.517842944'],\n", | |
| " dtype='datetime64[ns]', name='ping_time', freq=None))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>time1</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-78fc8049-1104-4d11-a857-a4a6fd68080a' class='xr-index-data-in' type='checkbox'/><label for='index-78fc8049-1104-4d11-a857-a4a6fd68080a' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(DatetimeIndex(['2023-10-03 12:00:51.976906240'], dtype='datetime64[ns]', name='time1', freq=None))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-48457c30-52f4-41ee-9c94-1934bfc258de' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-48457c30-52f4-41ee-9c94-1934bfc258de' class='xr-section-summary' title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>" | |
| ], | |
| "text/plain": [ | |
| "<xarray.DataArray 'sound_absorption' (time1: 1, channel: 2, ping_time: 63)>\n", | |
| "array([[[ nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan, 0.05424102, nan,\n", | |
| " 0.05424102, nan, 0.05424102, nan, 0.05424102,\n", | |
| " nan, 0.05424102, nan],\n", | |
| " [0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539, nan, 0.02356539,\n", | |
| " nan, 0.02356539, nan, 0.02356539, nan,\n", | |
| " 0.02356539, nan, 0.02356539]]])\n", | |
| "Coordinates:\n", | |
| " * channel (channel) <U33 'WBT Mini 274021-15-1 ES200-7C_ES' 'WBT Mini 27...\n", | |
| " * ping_time (ping_time) datetime64[ns] 2023-10-03T12:00:51.976906240 ... 2...\n", | |
| " * time1 (time1) datetime64[ns] 2023-10-03T12:00:51.976906240" | |
| ] | |
| }, | |
| "execution_count": 4, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "sound_absorption_da[\"sound_absorption\"].compute()" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "And now when we call the line in `harmonize_env_param_time` that caused the error, we end up with the following error in our attempt to squeeze:" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 5, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "ename": "IndexError", | |
| "evalue": "index 0 is out of bounds for axis 0 with size 0", | |
| "output_type": "error", | |
| "traceback": [ | |
| "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", | |
| "\u001b[0;31mIndexError\u001b[0m Traceback (most recent call last)", | |
| "Cell \u001b[0;32mIn[5], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43msound_absorption_da\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdropna\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdim\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mtime1\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msqueeze\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdim\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mtime1\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\u001b[38;5;241m.\u001b[39mdrop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtime1\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", | |
| "File \u001b[0;32m~/miniforge3/envs/echopype/lib/python3.9/site-packages/xarray/core/common.py:417\u001b[0m, in \u001b[0;36mDataWithCoords.squeeze\u001b[0;34m(self, dim, drop, axis)\u001b[0m\n\u001b[1;32m 392\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Return a new object with squeezed data.\u001b[39;00m\n\u001b[1;32m 393\u001b[0m \n\u001b[1;32m 394\u001b[0m \u001b[38;5;124;03mParameters\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 414\u001b[0m \u001b[38;5;124;03mnumpy.squeeze\u001b[39;00m\n\u001b[1;32m 415\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 416\u001b[0m dims \u001b[38;5;241m=\u001b[39m get_squeeze_dims(\u001b[38;5;28mself\u001b[39m, dim, axis)\n\u001b[0;32m--> 417\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43misel\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdrop\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdrop\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43m{\u001b[49m\u001b[43md\u001b[49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mfor\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43md\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01min\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mdims\u001b[49m\u001b[43m}\u001b[49m\u001b[43m)\u001b[49m\n", | |
| "File \u001b[0;32m~/miniforge3/envs/echopype/lib/python3.9/site-packages/xarray/core/dataset.py:2438\u001b[0m, in \u001b[0;36mDataset.isel\u001b[0;34m(self, indexers, drop, missing_dims, **indexers_kwargs)\u001b[0m\n\u001b[1;32m 2436\u001b[0m var_indexers \u001b[38;5;241m=\u001b[39m {k: v \u001b[38;5;28;01mfor\u001b[39;00m k, v \u001b[38;5;129;01min\u001b[39;00m indexers\u001b[38;5;241m.\u001b[39mitems() \u001b[38;5;28;01mif\u001b[39;00m k \u001b[38;5;129;01min\u001b[39;00m var\u001b[38;5;241m.\u001b[39mdims}\n\u001b[1;32m 2437\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m var_indexers:\n\u001b[0;32m-> 2438\u001b[0m var \u001b[38;5;241m=\u001b[39m \u001b[43mvar\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43misel\u001b[49m\u001b[43m(\u001b[49m\u001b[43mvar_indexers\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 2439\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m drop \u001b[38;5;129;01mand\u001b[39;00m var\u001b[38;5;241m.\u001b[39mndim \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m0\u001b[39m \u001b[38;5;129;01mand\u001b[39;00m name \u001b[38;5;129;01min\u001b[39;00m coord_names:\n\u001b[1;32m 2440\u001b[0m coord_names\u001b[38;5;241m.\u001b[39mremove(name)\n", | |
| "File \u001b[0;32m~/miniforge3/envs/echopype/lib/python3.9/site-packages/xarray/core/variable.py:1322\u001b[0m, in \u001b[0;36mVariable.isel\u001b[0;34m(self, indexers, missing_dims, **indexers_kwargs)\u001b[0m\n\u001b[1;32m 1319\u001b[0m indexers \u001b[38;5;241m=\u001b[39m drop_dims_from_indexers(indexers, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdims, missing_dims)\n\u001b[1;32m 1321\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mtuple\u001b[39m(indexers\u001b[38;5;241m.\u001b[39mget(dim, \u001b[38;5;28mslice\u001b[39m(\u001b[38;5;28;01mNone\u001b[39;00m)) \u001b[38;5;28;01mfor\u001b[39;00m dim \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdims)\n\u001b[0;32m-> 1322\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m[\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m]\u001b[49m\n", | |
| "File \u001b[0;32m~/miniforge3/envs/echopype/lib/python3.9/site-packages/xarray/core/variable.py:870\u001b[0m, in \u001b[0;36mVariable.__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 857\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Return a new Variable object whose contents are consistent with\u001b[39;00m\n\u001b[1;32m 858\u001b[0m \u001b[38;5;124;03mgetting the provided key from the underlying data.\u001b[39;00m\n\u001b[1;32m 859\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 867\u001b[0m \u001b[38;5;124;03marray `x.values` directly.\u001b[39;00m\n\u001b[1;32m 868\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 869\u001b[0m dims, indexer, new_order \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_broadcast_indexes(key)\n\u001b[0;32m--> 870\u001b[0m data \u001b[38;5;241m=\u001b[39m \u001b[43mas_indexable\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_data\u001b[49m\u001b[43m)\u001b[49m\u001b[43m[\u001b[49m\u001b[43mindexer\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 871\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m new_order:\n\u001b[1;32m 872\u001b[0m data \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39mmoveaxis(data, \u001b[38;5;28mrange\u001b[39m(\u001b[38;5;28mlen\u001b[39m(new_order)), new_order)\n", | |
| "File \u001b[0;32m~/miniforge3/envs/echopype/lib/python3.9/site-packages/xarray/core/indexing.py:657\u001b[0m, in \u001b[0;36mMemoryCachedArray.__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 656\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m__getitem__\u001b[39m(\u001b[38;5;28mself\u001b[39m, key):\n\u001b[0;32m--> 657\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mtype\u001b[39m(\u001b[38;5;28mself\u001b[39m)(_wrap_numpy_scalars(\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43marray\u001b[49m\u001b[43m[\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m]\u001b[49m))\n", | |
| "File \u001b[0;32m~/miniforge3/envs/echopype/lib/python3.9/site-packages/xarray/core/indexing.py:1264\u001b[0m, in \u001b[0;36mNumpyIndexingAdapter.__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 1262\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m__getitem__\u001b[39m(\u001b[38;5;28mself\u001b[39m, key):\n\u001b[1;32m 1263\u001b[0m array, key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_indexing_array_and_key(key)\n\u001b[0;32m-> 1264\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43marray\u001b[49m\u001b[43m[\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m]\u001b[49m\n", | |
| "\u001b[0;31mIndexError\u001b[0m: index 0 is out of bounds for axis 0 with size 0" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "sound_absorption_da.dropna(dim=\"time1\").squeeze(dim=\"time1\").drop(\"time1\")" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "This is because when we drop NaNs along this dimension, we are left with nothing since `time1`'s single dimension encapsulates the entire array with alternating NaNs and we cannot squeeze when nothing remains:" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
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| "</style><pre class='xr-text-repr-fallback'><xarray.Dataset>\n", | |
| "Dimensions: (channel: 2, ping_time: 63, time1: 0)\n", | |
| "Coordinates:\n", | |
| " * channel (channel) <U33 'WBT Mini 274021-15-1 ES200-7C_ES' 'WBT ...\n", | |
| " * ping_time (ping_time) datetime64[ns] 2023-10-03T12:00:51.97690624...\n", | |
| " * time1 (time1) datetime64[ns] \n", | |
| "Data variables:\n", | |
| " sound_absorption (time1, channel, ping_time) float64 </pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-e6d1821b-1476-4a02-97f3-a27cb4d8d507' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-e6d1821b-1476-4a02-97f3-a27cb4d8d507' class='xr-section-summary' title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>channel</span>: 2</li><li><span class='xr-has-index'>ping_time</span>: 63</li><li><span class='xr-has-index'>time1</span>: 0</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-e45a50a1-117f-481a-85ac-50ee21bba9c5' class='xr-section-summary-in' type='checkbox' checked><label for='section-e45a50a1-117f-481a-85ac-50ee21bba9c5' class='xr-section-summary' >Coordinates: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>channel</span></div><div class='xr-var-dims'>(channel)</div><div class='xr-var-dtype'><U33</div><div class='xr-var-preview xr-preview'>'WBT Mini 274021-15-1 ES200-7C_E...</div><input id='attrs-f0bdff2c-dafc-45f8-9eb8-3671dba866f6' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f0bdff2c-dafc-45f8-9eb8-3671dba866f6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-35771b11-9baa-4812-aff5-24e1caadb74a' class='xr-var-data-in' type='checkbox'><label for='data-35771b11-9baa-4812-aff5-24e1caadb74a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Vendor channel ID</dd></dl></div><div class='xr-var-data'><pre>array(['WBT Mini 274021-15-1 ES200-7C_ES', 'WBT Mini 274021-15-2 ES70-18CD_ES'],\n", | |
| " dtype='<U33')</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>ping_time</span></div><div class='xr-var-dims'>(ping_time)</div><div class='xr-var-dtype'>datetime64[ns]</div><div class='xr-var-preview xr-preview'>2023-10-03T12:00:51.976906240 .....</div><input id='attrs-d9d96b0b-0a8e-4f57-938d-918741234da0' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d9d96b0b-0a8e-4f57-938d-918741234da0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-edc365fe-ad4f-4f86-8ff9-cd5307838b17' class='xr-var-data-in' type='checkbox'><label for='data-edc365fe-ad4f-4f86-8ff9-cd5307838b17' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>axis :</span></dt><dd>T</dd><dt><span>long_name :</span></dt><dd>Timestamp of each ping</dd><dt><span>standard_name :</span></dt><dd>time</dd></dl></div><div class='xr-var-data'><pre>array(['2023-10-03T12:00:51.976906240', '2023-10-03T12:00:53.559627776',\n", | |
| " '2023-10-03T12:00:54.005223936', '2023-10-03T12:00:55.562006016',\n", | |
| " '2023-10-03T12:00:56.009693184', '2023-10-03T12:00:57.569653248',\n", | |
| " '2023-10-03T12:00:57.993319936', '2023-10-03T12:00:59.553221120',\n", | |
| " '2023-10-03T12:01:00.363073024', '2023-10-03T12:01:01.922873856',\n", | |
| " '2023-10-03T12:01:02.371548160', '2023-10-03T12:01:03.949699072',\n", | |
| " '2023-10-03T12:01:04.401380864', '2023-10-03T12:01:05.950732800',\n", | |
| " '2023-10-03T12:01:06.407278080', '2023-10-03T12:01:07.965466112',\n", | |
| " '2023-10-03T12:01:08.388156928', '2023-10-03T12:01:09.937934848',\n", | |
| " '2023-10-03T12:01:10.748850176', '2023-10-03T12:01:12.291490816',\n", | |
| " '2023-10-03T12:01:12.745195008', '2023-10-03T12:01:14.304367104',\n", | |
| " '2023-10-03T12:01:14.748951040', '2023-10-03T12:01:16.317727744',\n", | |
| " '2023-10-03T12:01:16.772888064', '2023-10-03T12:01:18.330081792',\n", | |
| " '2023-10-03T12:01:18.751777792', '2023-10-03T12:01:20.304416768',\n", | |
| " '2023-10-03T12:01:21.177158144', '2023-10-03T12:01:22.737865216',\n", | |
| " '2023-10-03T12:01:23.196512256', '2023-10-03T12:01:24.772293120',\n", | |
| " '2023-10-03T12:01:25.233106944', '2023-10-03T12:01:26.794712064',\n", | |
| " '2023-10-03T12:01:27.250378240', '2023-10-03T12:01:28.811527168',\n", | |
| " '2023-10-03T12:01:29.245244928', '2023-10-03T12:01:30.821850112',\n", | |
| " '2023-10-03T12:01:31.646898176', '2023-10-03T12:01:33.201689088',\n", | |
| " '2023-10-03T12:01:33.640371200', '2023-10-03T12:01:35.215869952',\n", | |
| " '2023-10-03T12:01:35.653824000', '2023-10-03T12:01:37.228828160',\n", | |
| " '2023-10-03T12:01:37.674447872', '2023-10-03T12:01:39.242184192',\n", | |
| " '2023-10-03T12:01:39.659781120', '2023-10-03T12:01:41.244993024',\n", | |
| " '2023-10-03T12:01:42.054491136', '2023-10-03T12:01:43.603165184',\n", | |
| " '2023-10-03T12:01:44.049811968', '2023-10-03T12:01:45.620483072',\n", | |
| " '2023-10-03T12:01:46.073785856', '2023-10-03T12:01:47.643970048',\n", | |
| " '2023-10-03T12:01:48.087618048', '2023-10-03T12:01:49.635296256',\n", | |
| " '2023-10-03T12:01:50.058952192', '2023-10-03T12:01:51.644869120',\n", | |
| " '2023-10-03T12:01:52.455427072', '2023-10-03T12:01:54.007105024',\n", | |
| " '2023-10-03T12:01:54.474840064', '2023-10-03T12:01:56.051064832',\n", | |
| " '2023-10-03T12:01:56.517842944'], dtype='datetime64[ns]')</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>time1</span></div><div class='xr-var-dims'>(time1)</div><div class='xr-var-dtype'>datetime64[ns]</div><div class='xr-var-preview xr-preview'></div><input id='attrs-2d4d42a5-0a32-4546-9de6-c17532920334' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-2d4d42a5-0a32-4546-9de6-c17532920334' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5c0cf2e1-a09a-43da-ba26-0c83e26287cc' class='xr-var-data-in' type='checkbox'><label for='data-5c0cf2e1-a09a-43da-ba26-0c83e26287cc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>axis :</span></dt><dd>T</dd><dt><span>comment :</span></dt><dd>Time coordinate corresponding to environmental variables. Note that Platform.time3 is the same as Environment.time1.</dd><dt><span>long_name :</span></dt><dd>Timestamps for NMEA position datagrams</dd><dt><span>standard_name :</span></dt><dd>time</dd></dl></div><div class='xr-var-data'><pre>array([], dtype='datetime64[ns]')</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-de169c11-a227-4133-8777-31cc11e2a745' class='xr-section-summary-in' type='checkbox' checked><label for='section-de169c11-a227-4133-8777-31cc11e2a745' class='xr-section-summary' >Data variables: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sound_absorption</span></div><div class='xr-var-dims'>(time1, channel, ping_time)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'></div><input id='attrs-80f39859-3cf8-4259-bbd8-e0617370d5b8' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-80f39859-3cf8-4259-bbd8-e0617370d5b8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-92786e9e-d7fb-4974-aefb-e815723c861b' class='xr-var-data-in' type='checkbox'><label for='data-92786e9e-d7fb-4974-aefb-e815723c861b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([], shape=(0, 2, 63), dtype=float64)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-807c0049-991a-4794-92ce-c3351deb4e62' class='xr-section-summary-in' type='checkbox' ><label for='section-807c0049-991a-4794-92ce-c3351deb4e62' class='xr-section-summary' >Indexes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>channel</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-d1abbd9f-1177-4d11-976a-51f7d40b101c' class='xr-index-data-in' type='checkbox'/><label for='index-d1abbd9f-1177-4d11-976a-51f7d40b101c' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index(['WBT Mini 274021-15-1 ES200-7C_ES', 'WBT Mini 274021-15-2 ES70-18CD_ES'], dtype='object', name='channel'))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>ping_time</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-7671e551-221a-45f2-9d2b-821693df6567' class='xr-index-data-in' type='checkbox'/><label for='index-7671e551-221a-45f2-9d2b-821693df6567' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(DatetimeIndex(['2023-10-03 12:00:51.976906240',\n", | |
| " '2023-10-03 12:00:53.559627776',\n", | |
| " '2023-10-03 12:00:54.005223936',\n", | |
| " '2023-10-03 12:00:55.562006016',\n", | |
| " '2023-10-03 12:00:56.009693184',\n", | |
| " '2023-10-03 12:00:57.569653248',\n", | |
| " '2023-10-03 12:00:57.993319936',\n", | |
| " '2023-10-03 12:00:59.553221120',\n", | |
| " '2023-10-03 12:01:00.363073024',\n", | |
| " '2023-10-03 12:01:01.922873856',\n", | |
| " '2023-10-03 12:01:02.371548160',\n", | |
| " '2023-10-03 12:01:03.949699072',\n", | |
| " '2023-10-03 12:01:04.401380864',\n", | |
| " '2023-10-03 12:01:05.950732800',\n", | |
| " '2023-10-03 12:01:06.407278080',\n", | |
| " '2023-10-03 12:01:07.965466112',\n", | |
| " '2023-10-03 12:01:08.388156928',\n", | |
| " '2023-10-03 12:01:09.937934848',\n", | |
| " '2023-10-03 12:01:10.748850176',\n", | |
| " '2023-10-03 12:01:12.291490816',\n", | |
| " '2023-10-03 12:01:12.745195008',\n", | |
| " '2023-10-03 12:01:14.304367104',\n", | |
| " '2023-10-03 12:01:14.748951040',\n", | |
| " '2023-10-03 12:01:16.317727744',\n", | |
| " '2023-10-03 12:01:16.772888064',\n", | |
| " '2023-10-03 12:01:18.330081792',\n", | |
| " '2023-10-03 12:01:18.751777792',\n", | |
| " '2023-10-03 12:01:20.304416768',\n", | |
| " '2023-10-03 12:01:21.177158144',\n", | |
| " '2023-10-03 12:01:22.737865216',\n", | |
| " '2023-10-03 12:01:23.196512256',\n", | |
| " '2023-10-03 12:01:24.772293120',\n", | |
| " '2023-10-03 12:01:25.233106944',\n", | |
| " '2023-10-03 12:01:26.794712064',\n", | |
| " '2023-10-03 12:01:27.250378240',\n", | |
| " '2023-10-03 12:01:28.811527168',\n", | |
| " '2023-10-03 12:01:29.245244928',\n", | |
| " '2023-10-03 12:01:30.821850112',\n", | |
| " '2023-10-03 12:01:31.646898176',\n", | |
| " '2023-10-03 12:01:33.201689088',\n", | |
| " '2023-10-03 12:01:33.640371200',\n", | |
| " '2023-10-03 12:01:35.215869952',\n", | |
| " '2023-10-03 12:01:35.653824',\n", | |
| " '2023-10-03 12:01:37.228828160',\n", | |
| " '2023-10-03 12:01:37.674447872',\n", | |
| " '2023-10-03 12:01:39.242184192',\n", | |
| " '2023-10-03 12:01:39.659781120',\n", | |
| " '2023-10-03 12:01:41.244993024',\n", | |
| " '2023-10-03 12:01:42.054491136',\n", | |
| " '2023-10-03 12:01:43.603165184',\n", | |
| " '2023-10-03 12:01:44.049811968',\n", | |
| " '2023-10-03 12:01:45.620483072',\n", | |
| " '2023-10-03 12:01:46.073785856',\n", | |
| " '2023-10-03 12:01:47.643970048',\n", | |
| " '2023-10-03 12:01:48.087618048',\n", | |
| " '2023-10-03 12:01:49.635296256',\n", | |
| " '2023-10-03 12:01:50.058952192',\n", | |
| " '2023-10-03 12:01:51.644869120',\n", | |
| " '2023-10-03 12:01:52.455427072',\n", | |
| " '2023-10-03 12:01:54.007105024',\n", | |
| " '2023-10-03 12:01:54.474840064',\n", | |
| " '2023-10-03 12:01:56.051064832',\n", | |
| " '2023-10-03 12:01:56.517842944'],\n", | |
| " dtype='datetime64[ns]', name='ping_time', freq=None))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>time1</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-a3b0b4c2-12c7-430b-98c6-f60ec44f98bb' class='xr-index-data-in' type='checkbox'/><label for='index-a3b0b4c2-12c7-430b-98c6-f60ec44f98bb' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(DatetimeIndex([], dtype='datetime64[ns]', name='time1', freq=None))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-a88bbefb-b57e-4ce6-acaa-b2cc116eb5f5' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-a88bbefb-b57e-4ce6-acaa-b2cc116eb5f5' class='xr-section-summary' title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>" | |
| ], | |
| "text/plain": [ | |
| "<xarray.Dataset>\n", | |
| "Dimensions: (channel: 2, ping_time: 63, time1: 0)\n", | |
| "Coordinates:\n", | |
| " * channel (channel) <U33 'WBT Mini 274021-15-1 ES200-7C_ES' 'WBT ...\n", | |
| " * ping_time (ping_time) datetime64[ns] 2023-10-03T12:00:51.97690624...\n", | |
| " * time1 (time1) datetime64[ns] \n", | |
| "Data variables:\n", | |
| " sound_absorption (time1, channel, ping_time) float64 " | |
| ] | |
| }, | |
| "execution_count": 9, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "sound_absorption_da.dropna(dim=\"time1\")" | |
| ] | |
| } | |
| ], | |
| "metadata": { | |
| "kernelspec": { | |
| "display_name": "echopype", | |
| "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": "3.9.18" | |
| } | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 2 | |
| } |
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