big update

remove .ds_store
update jan 1

.gitignore

@@ -5,4 +5,7 @@ index.html
 *.nc
 *.csv
 jupyterbook/content/code_gallery/ecofoci_field*/*/*/*.png
-jupyterbook/content/code_gallery/ecofoci_fielddata_history/.DS_Store
+.DS_Store
+._.DS_Store
+**/.DS_Store
+**/._.DS_Store

jupyterbook/content/code_gallery/ecofoci_fielddata_history/cruises/2024/EcoFOCIpy_sbe_ctd_btlfile_DY2410.ipynb

@@ -3029,7 +3029,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.1"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

jupyterbook/content/code_gallery/ecofoci_fielddata_history/cruises/2024/EcoFOCIpy_sbe_ctd_dy2407_QC.ipynb

@@ -22,15 +22,27 @@
     "***TODO:***\n",
     "+ Add ability to specify cast/instrument and make all values missing/removed\n",
     "+ Add ability to linearly interpolate between singleton points in profile for speciffic parameters\n",
-    "+ Update any meta data "
+    "+ Update any meta data\n",
+    "\n",
+    "***Changes from previous cruises:***\n",
+    "+ use GSW instead of SW for dens0 calculation"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 1,
    "id": "studied-pollution",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/bell/src/ecofocipy/src/EcoFOCIpy/plots/sbe_ctd_plots.py:10: UserWarning: The seawater library is deprecated! Please use gsw instead.\n",
+      "  import seawater as sw\n"
+     ]
+    }
+   ],
    "source": [
     "import os\n",
     "import numpy as np\n",
@@ -77,16 +89,33 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 27,
    "id": "62303737-7588-498d-84dc-8fdc784358a9",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Following routines will eventually get ported to ecofocipy as subroutines to be called\n",
     "\n",
-    "import seawater as sw\n",
+    "import gsw_xarray as gsw\n",
     "\n",
-    "def sigmat_update(salinity=None,temperature=None):\n",
+    "def sigmat_update(salinity=None,temperature=None,depth=None,latitude=0,longitude=0):\n",
+    "    r'''\n",
+    "    Changes to T or S (commonly to despike values or apply a salinity offset) will need corresponding changes in sigmat.\n",
+    "    Calculation uses Gibbs-Seawater\n",
+    "    '''\n",
+    "    SA = gsw.SA_from_SP(SP=salinity,\n",
+    "                      p=depth,\n",
+    "                      lat=latitude,\n",
+    "                      lon=longitude)\n",
+    "    CT = gsw.CT_from_t(SA,\n",
+    "                      temperature,\n",
+    "                      depth)\n",
+    "    \n",
+    "    dens0 = gsw.density.sigma0(SA,CT)\n",
+    "\n",
+    "    return dens0\n",
+    "    \n",
+    "def sigmat_update_old(salinity=None,temperature=None):\n",
     "    '''\n",
     "    Changes to T or S (commonly to despike values or apply a salinity offset) will need corresponding changes in sigmat\n",
     "    '''\n",
@@ -96,7 +125,7 @@
     "    return sigt\n",
     "\n",
     "\n",
-    "def oxyconc_update(salinity=None,temperature=None, oxygen_conc_umkg=None,pressure=None):\n",
+    "def oxyconc_update(salinity=None,temperature=None, oxygen_conc_umkg=None,pressure=None,sigmatheta_pri=0):\n",
     "    '''\n",
     "        Although PJS tends to look at %sat to QC, changes are usually applied on the concentration parameter. So %sat will need recalculation.\n",
     "        Changes to T/S also drive some small corrections.\n",
@@ -137,15 +166,15 @@
     "    \n",
     "    # determine sigmatheta and convert Oxygen from micromoles/kg to ml/l\n",
     "    # calculate new oxygen saturation percent using derived oxsol\n",
-    "    sigmatheta_pri = sw.eos80.pden(s=salinity, t=temperature, p=pressure)\n",
+    "    # sigmatheta_pri = sw.eos80.pden(s=salinity, t=temperature, p=pressure)\n",
     "    oxygen_conc_mll = oxygen_conc_umkg * sigmatheta_pri / 44660\n",
     "    \n",
     "    return oxygen_conc_mll,((oxygen_conc_mll) / Oxsol_pri) * 100.0, oxygen_conc_umkg"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 33,
    "id": "a11505a2-6f36-454b-8f46-d5c54c479526",
    "metadata": {
     "tags": []
@@ -156,16 +185,18 @@
      "output_type": "stream",
      "text": [
       "Updated: DY2407c001_ctd.nc\n",
-      "Updated: DY2407c002_ctd.nc\n"
+      "No file to update: DY2407c001_ctd.updated.nc\n",
+      "Updated: DY2407c002_ctd.nc\n",
+      "No file to update: DY2407c002_ctd.updated.nc\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/var/folders/6r/n_mpcj7d7pdf9ncqvjy5vb8c0000jm/T/ipykernel_12735/397792649.py:39: UserWarning: Times can't be serialized faithfully to int64 with requested units 'days since 1900-01-01'. Resolution of 'minutes' needed. Serializing times to floating point instead. Set encoding['dtype'] to integer dtype to serialize to int64. Set encoding['dtype'] to floating point dtype to silence this warning.\n",
+      "/var/folders/6r/n_mpcj7d7pdf9ncqvjy5vb8c0000jm/T/ipykernel_11935/560199972.py:39: UserWarning: Times can't be serialized faithfully to int64 with requested units 'days since 1900-01-01'. Resolution of 'minutes' needed. Serializing times to floating point instead. Set encoding['dtype'] to integer dtype to serialize to int64. Set encoding['dtype'] to floating point dtype to silence this warning.\n",
       "  cruise_data_update.to_netcdf(sample_data_dir+cast.replace(ncfiles,'.updated.nc'),format='NETCDF3_CLASSIC',encoding={'time':{'units':'days since 1900-01-01'}})\n",
-      "/var/folders/6r/n_mpcj7d7pdf9ncqvjy5vb8c0000jm/T/ipykernel_12735/397792649.py:39: UserWarning: Times can't be serialized faithfully to int64 with requested units 'days since 1900-01-01'. Resolution of 'minutes' needed. Serializing times to floating point instead. Set encoding['dtype'] to integer dtype to serialize to int64. Set encoding['dtype'] to floating point dtype to silence this warning.\n",
+      "/var/folders/6r/n_mpcj7d7pdf9ncqvjy5vb8c0000jm/T/ipykernel_11935/560199972.py:39: UserWarning: Times can't be serialized faithfully to int64 with requested units 'days since 1900-01-01'. Resolution of 'minutes' needed. Serializing times to floating point instead. Set encoding['dtype'] to integer dtype to serialize to int64. Set encoding['dtype'] to floating point dtype to silence this warning.\n",
       "  cruise_data_update.to_netcdf(sample_data_dir+cast.replace(ncfiles,'.updated.nc'),format='NETCDF3_CLASSIC',encoding={'time':{'units':'days since 1900-01-01'}})\n"
      ]
     }
@@ -185,14 +216,14 @@
     "                \n",
     "            #update sigmat (or calculate it I suppose)\n",
     "            sigup = sigmat_update(salinity=pandas_csv.salinity_ch1,\n",
-    "                                  temperature=pandas_csv.temperature_ch1)\n",
-    "            cruise_data_update['sigma_t_ch1'] = (['time','latitude','longitude','depth'],(sigup * 0) +  np.nan)\n",
-    "            cruise_data_update['sigma_t_ch1'].values = sigup\n",
+    "                                  temperature=pandas_csv.temperature_ch1,\n",
+    "                                  depth=pandas_csv.depth)\n",
+    "            cruise_data_update['sigma_t_ch1'] = sigup\n",
     "            \n",
     "            sigup2 = sigmat_update(salinity=pandas_csv.salinity_ch2,\n",
-    "                                  temperature=pandas_csv.temperature_ch2)\n",
-    "            cruise_data_update['sigma_t_ch2'] = (['time','latitude','longitude','depth'],(sigup2 * 0) +  np.nan)\n",
-    "            cruise_data_update['sigma_t_ch2'].values = sigup2   \n",
+    "                                  temperature=pandas_csv.temperature_ch2,\n",
+    "                                  depth=pandas_csv.depth)\n",
+    "            cruise_data_update['sigma_t_ch2'] = sigup2\n",
     "            \n",
     "            #update \n",
     "            #need to update any other oxy conc units too\n",
@@ -328,9 +359,9 @@
    "hash": "bc96f01bfc9d2c897ec898f99e5079e1d7ab4b93a6c269a5e00afdb6d52f3b37"
   },
   "kernelspec": {
-   "display_name": "Python [conda env:py311] *",
+   "display_name": "Python [conda env:p312]",
    "language": "python",
-   "name": "conda-env-py311-py"
+   "name": "conda-env-p312-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -342,7 +373,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.10"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

jupyterbook/content/code_gallery/ecofoci_fielddata_history/cruises/2024/EcoFOCIpy_sbe_ctd_oxy_dy2407_simple.ipynb

@@ -7,15 +7,15 @@
    "source": [
     "# Using EcoFOCIpy to process raw field data\n",
     "\n",
-    "## DY2410 (Fall Mooring Cruise - Dyson)\n",
+    "## DY2407 (Spring Mooring Cruise - Dyson)\n",
     "\n",
     "## BO Oxygen Data\n",
     "\n"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 5,
    "id": "studied-pollution",
    "metadata": {
     "tags": []
@@ -34,7 +34,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 6,
    "id": "offensive-level",
    "metadata": {
     "tags": []
@@ -47,7 +47,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 7,
    "id": "third-yellow",
    "metadata": {
     "tags": []
@@ -100,7 +100,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 8,
    "id": "f0fb5c09-d76d-455c-89f4-3ba6a7954f00",
    "metadata": {
     "tags": []
@@ -217,43 +217,29 @@
        "      <td>7</td>\n",
        "      <td>414.924500</td>\n",
        "    </tr>\n",
-       "    <tr>\n",
-       "      <th>14</th>\n",
-       "      <td>5/20/2024</td>\n",
-       "      <td>1148</td>\n",
-       "      <td>444.936998</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>15</th>\n",
-       "      <td>5/24/2024</td>\n",
-       "      <td>440</td>\n",
-       "      <td>422.563636</td>\n",
-       "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
        "</div>"
       ],
       "text/plain": [
-       "         Cast  Niskin     O2 (uM)\n",
-       "0           1       1  378.676337\n",
-       "1           1       2  360.325790\n",
-       "2           1       3  391.045738\n",
-       "3           1       4  403.876479\n",
-       "4           1       5  410.724907\n",
-       "5           1       6  441.293469\n",
-       "6           1       7  447.402320\n",
-       "7           2       1  387.668718\n",
-       "8           2       2  379.812731\n",
-       "9           2       3  371.404091\n",
-       "10          2       4  372.886771\n",
-       "11          2       5  393.445621\n",
-       "12          2       6  415.333062\n",
-       "13          2       7  414.924500\n",
-       "14  5/20/2024    1148  444.936998\n",
-       "15  5/24/2024     440  422.563636"
+       "    Cast  Niskin     O2 (uM)\n",
+       "0      1       1  378.676337\n",
+       "1      1       2  360.325790\n",
+       "2      1       3  391.045738\n",
+       "3      1       4  403.876479\n",
+       "4      1       5  410.724907\n",
+       "5      1       6  441.293469\n",
+       "6      1       7  447.402320\n",
+       "7      2       1  387.668718\n",
+       "8      2       2  379.812731\n",
+       "9      2       3  371.404091\n",
+       "10     2       4  372.886771\n",
+       "11     2       5  393.445621\n",
+       "12     2       6  415.333062\n",
+       "13     2       7  414.924500"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 8,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -265,7 +251,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 9,
    "id": "ec15a06d-f7e3-4a0e-880a-2bb48beef0bd",
    "metadata": {},
    "outputs": [],
@@ -283,7 +269,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 10,
    "id": "586c00a1-4b89-4488-927c-a9d84df24225",
    "metadata": {
     "tags": []
@@ -311,7 +297,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 11,
    "id": "freelance-fairy",
    "metadata": {
     "tags": []
@@ -336,7 +322,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 12,
    "id": "checked-raise",
    "metadata": {
     "tags": []
@@ -357,7 +343,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 13,
    "id": "24b2c8b0",
    "metadata": {
     "tags": []
@@ -380,7 +366,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 14,
    "id": "modular-volunteer",
    "metadata": {
     "scrolled": true,