Merge pull request #6 from jukent/reuse

code reuse

notebooks/display_source.py

@@ -0,0 +1,12 @@
+from IPython.display import display, HTML
+from pygments import highlight
+from pygments.lexers import PythonLexer
+from pygments.formatters import HtmlFormatter
+import inspect
+
+def display_source(obj, color=True):
+    obj_src = inspect.getsource(obj)
+    if color:
+        display(HTML(highlight(obj_src, PythonLexer(), HtmlFormatter())))
+    else:
+        print(obj_src)

notebooks/module.py

@@ -0,0 +1,57 @@
+import numpy as np
+
+def adjust_pop_grid(tlon,tlat,field):
+    """
+    Adjusts the grid of longitude and latitude values, along with the corresponding field data.
+
+    Parameters
+    ----------
+    tlon : numpy.ndarray
+        2D array of longitude values.
+    tlat : numpy.ndarray
+        2D array of latitude values.
+    field : numpy.ma.MaskedArray
+        2D array of field data (e.g., temperature, salinity) corresponding to the tlon and tlat arrays.
+
+    Returns
+    -------
+    lon : numpy.ndarray
+        Adjusted 2D array of longitude values.
+    lat : numpy.ndarray
+        Adjusted 2D array of latitude values.
+    field : numpy.ma.MaskedArray
+        Adjusted 2D array of field data.
+
+    Example
+    -------
+    >>> lon, lat, field = adjust_pop_grid(tlon, tlat, field)
+    """
+    nj = tlon.shape[0]
+    ni = tlon.shape[1]
+    xL = int(ni/2 - 1)
+    xR = int(xL + ni)
+
+    tlon = np.where(np.greater_equal(tlon,min(tlon[:,0])),tlon-360.,tlon)
+    lon  = np.concatenate((tlon,tlon+360.),1)
+    lon = lon[:,xL:xR]
+
+    if ni == 320:
+        lon[367:-3,0] = lon[367:-3,0]+360.
+    lon = lon - 360.
+    lon = np.hstack((lon,lon[:,0:1]+360.))
+    if ni == 320:
+        lon[367:,-1] = lon[367:,-1] - 360.
+
+    # Trick cartopy into doing the right thing:
+    # it gets confused when the cyclic coords are identical
+    lon[:,0] = lon[:,0]-1e-8
+
+    # Periodicity
+    lat  = np.concatenate((tlat,tlat),1)
+    lat = lat[:,xL:xR]
+    lat = np.hstack((lat,lat[:,0:1]))
+
+    field = np.ma.concatenate((field,field),1)
+    field = field[:,xL:xR]
+    field = np.ma.hstack((field,field[:,0:1]))
+    return lon,lat,field

notebooks/ocn-carbonfluxes.ipynb

@@ -89,7 +89,9 @@
     "import dask\n",
     "import distributed\n",
     "import s3fs\n",
-    "import netCDF4"
+    "import netCDF4\n",
+    "\n",
+    "from module import adjust_pop_grid"
    ]
   },
   {
@@ -150,45 +152,6 @@
     "ds_grid"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "d1f1efc5-a878-4d00-bbac-d0185863bea3",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def adjust_pop_grid(tlon,tlat,field):\n",
-    "    nj = tlon.shape[0]\n",
-    "    ni = tlon.shape[1]\n",
-    "    xL = int(ni/2 - 1)\n",
-    "    xR = int(xL + ni)\n",
-    "\n",
-    "    tlon = np.where(np.greater_equal(tlon,min(tlon[:,0])),tlon-360.,tlon)\n",
-    "    lon  = np.concatenate((tlon,tlon+360.),1)\n",
-    "    lon = lon[:,xL:xR]\n",
-    "\n",
-    "    if ni == 320:\n",
-    "        lon[367:-3,0] = lon[367:-3,0]+360.\n",
-    "    lon = lon - 360.\n",
-    "    lon = np.hstack((lon,lon[:,0:1]+360.))\n",
-    "    if ni == 320:\n",
-    "        lon[367:,-1] = lon[367:,-1] - 360.\n",
-    "\n",
-    "    # Trick cartopy into doing the right thing:\n",
-    "    # it gets confused when the cyclic coords are identical\n",
-    "    lon[:,0] = lon[:,0]-1e-8\n",
-    "    \n",
-    "    # Periodicity\n",
-    "    lat  = np.concatenate((tlat,tlat),1)\n",
-    "    lat = lat[:,xL:xR]\n",
-    "    lat = np.hstack((lat,lat[:,0:1]))\n",
-    "\n",
-    "    field = np.ma.concatenate((field,field),1)\n",
-    "    field = field[:,xL:xR]\n",
-    "    field = np.ma.hstack((field,field[:,0:1]))\n",
-    "    return lon,lat,field"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "2cdc4f48-ec2a-4f63-a309-53803f476f7b",

notebooks/ocn-iron.ipynb

@@ -81,7 +81,9 @@
     "from dask.distributed import LocalCluster\n",
     "import pandas as pd\n",
     "import s3fs\n",
-    "import netCDF4"
+    "import netCDF4\n",
+    "\n",
+    "from module import adjust_pop_grid"
    ]
   },
   {
@@ -132,45 +134,6 @@
     "depths = ds_grid.z_t * 0.01"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "78660a8f-98bd-4f6a-b8f1-448d06787854",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def adjust_pop_grid(tlon,tlat,field):\n",
-    "    nj = tlon.shape[0]\n",
-    "    ni = tlon.shape[1]\n",
-    "    xL = int(ni/2 - 1)\n",
-    "    xR = int(xL + ni)\n",
-    "\n",
-    "    tlon = np.where(np.greater_equal(tlon,min(tlon[:,0])),tlon-360.,tlon)\n",
-    "    lon  = np.concatenate((tlon,tlon+360.),1)\n",
-    "    lon = lon[:,xL:xR]\n",
-    "\n",
-    "    if ni == 320:\n",
-    "        lon[367:-3,0] = lon[367:-3,0]+360.\n",
-    "    lon = lon - 360.\n",
-    "    lon = np.hstack((lon,lon[:,0:1]+360.))\n",
-    "    if ni == 320:\n",
-    "        lon[367:,-1] = lon[367:,-1] - 360.\n",
-    "\n",
-    "    # Trick cartopy into doing the right thing:\n",
-    "    # it gets confused when the cyclic coords are identical\n",
-    "    lon[:,0] = lon[:,0]-1e-8\n",
-    "    \n",
-    "    # Periodicity\n",
-    "    lat  = np.concatenate((tlat,tlat),1)\n",
-    "    lat = lat[:,xL:xR]\n",
-    "    lat = np.hstack((lat,lat[:,0:1]))\n",
-    "\n",
-    "    field = np.ma.concatenate((field,field),1)\n",
-    "    field = field[:,xL:xR]\n",
-    "    field = np.ma.hstack((field,field[:,0:1]))\n",
-    "    return lon,lat,field"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "3630bab7-a9ea-4433-9eb8-f8555cab07bd",

notebooks/ocn-macronuts.ipynb

@@ -86,7 +86,9 @@
     "import pop_tools\n",
     "from dask.distributed import LocalCluster\n",
     "import s3fs\n",
-    "import netCDF4"
+    "import netCDF4\n",
+    "\n",
+    "from module import adjust_pop_grid"
    ]
   },
   {
@@ -157,45 +159,6 @@
     "depths = ds_grid.z_t * 0.01"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "5d56f6ba-7bdb-43bd-b8ad-badbf5a112b1",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def adjust_pop_grid(tlon,tlat,field):\n",
-    "    nj = tlon.shape[0]\n",
-    "    ni = tlon.shape[1]\n",
-    "    xL = int(ni/2 - 1)\n",
-    "    xR = int(xL + ni)\n",
-    "\n",
-    "    tlon = np.where(np.greater_equal(tlon,min(tlon[:,0])),tlon-360.,tlon)\n",
-    "    lon  = np.concatenate((tlon,tlon+360.),1)\n",
-    "    lon = lon[:,xL:xR]\n",
-    "\n",
-    "    if ni == 320:\n",
-    "        lon[367:-3,0] = lon[367:-3,0]+360.\n",
-    "    lon = lon - 360.\n",
-    "    lon = np.hstack((lon,lon[:,0:1]+360.))\n",
-    "    if ni == 320:\n",
-    "        lon[367:,-1] = lon[367:,-1] - 360.\n",
-    "\n",
-    "    # Trick cartopy into doing the right thing:\n",
-    "    # it gets confused when the cyclic coords are identical\n",
-    "    lon[:,0] = lon[:,0]-1e-8\n",
-    "    \n",
-    "    # Periodicity\n",
-    "    lat  = np.concatenate((tlat,tlat),1)\n",
-    "    lat = lat[:,xL:xR]\n",
-    "    lat = np.hstack((lat,lat[:,0:1]))\n",
-    "\n",
-    "    field = np.ma.concatenate((field,field),1)\n",
-    "    field = field[:,xL:xR]\n",
-    "    field = np.ma.hstack((field,field[:,0:1]))\n",
-    "    return lon,lat,field"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "976ffa95-263e-4d11-bda3-0637f9d28212",

notebooks/ocn-phyto-biomass.ipynb

@@ -95,7 +95,9 @@
     "from dask.distributed import LocalCluster\n",
     "import s3fs\n",
     "import netCDF4\n",
-    "from datetime import datetime"
+    "from datetime import datetime\n",
+    "\n",
+    "from module import adjust_pop_grid"
    ]
   },
   {
@@ -146,45 +148,6 @@
     "depths = ds_grid.z_t * 0.01"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7cf6b5c7-15fb-44a1-bc31-af0666433995",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def adjust_pop_grid(tlon,tlat,field):\n",
-    "    nj = tlon.shape[0]\n",
-    "    ni = tlon.shape[1]\n",
-    "    xL = int(ni/2 - 1)\n",
-    "    xR = int(xL + ni)\n",
-    "\n",
-    "    tlon = np.where(np.greater_equal(tlon,min(tlon[:,0])),tlon-360.,tlon)\n",
-    "    lon  = np.concatenate((tlon,tlon+360.),1)\n",
-    "    lon = lon[:,xL:xR]\n",
-    "\n",
-    "    if ni == 320:\n",
-    "        lon[367:-3,0] = lon[367:-3,0]+360.\n",
-    "    lon = lon - 360.\n",
-    "    lon = np.hstack((lon,lon[:,0:1]+360.))\n",
-    "    if ni == 320:\n",
-    "        lon[367:,-1] = lon[367:,-1] - 360.\n",
-    "\n",
-    "    # Trick cartopy into doing the right thing:\n",
-    "    # it gets confused when the cyclic coords are identical\n",
-    "    lon[:,0] = lon[:,0]-1e-8\n",
-    "    \n",
-    "    # Periodicity\n",
-    "    lat  = np.concatenate((tlat,tlat),1)\n",
-    "    lat = lat[:,xL:xR]\n",
-    "    lat = np.hstack((lat,lat[:,0:1]))\n",
-    "\n",
-    "    field = np.ma.concatenate((field,field),1)\n",
-    "    field = field[:,xL:xR]\n",
-    "    field = np.ma.hstack((field,field[:,0:1]))\n",
-    "    return lon,lat,field"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "e2eda11b-15e6-471f-8d09-e07f62a1710d",

notebooks/ocn-phyto-lims.ipynb

@@ -94,7 +94,9 @@
     "import pop_tools\n",
     "from dask.distributed import LocalCluster\n",
     "import s3fs\n",
-    "import netCDF4"
+    "import netCDF4\n",
+    "\n",
+    "from module import adjust_pop_grid"
    ]
   },
   {
@@ -145,45 +147,6 @@
     "depths = ds_grid.z_t * 0.01"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "0b73860c-5a37-42b7-bd8c-7c841937e0b6",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def adjust_pop_grid(tlon,tlat,field):\n",
-    "    nj = tlon.shape[0]\n",
-    "    ni = tlon.shape[1]\n",
-    "    xL = int(ni/2 - 1)\n",
-    "    xR = int(xL + ni)\n",
-    "\n",
-    "    tlon = np.where(np.greater_equal(tlon,min(tlon[:,0])),tlon-360.,tlon)\n",
-    "    lon  = np.concatenate((tlon,tlon+360.),1)\n",
-    "    lon = lon[:,xL:xR]\n",
-    "\n",
-    "    if ni == 320:\n",
-    "        lon[367:-3,0] = lon[367:-3,0]+360.\n",
-    "    lon = lon - 360.\n",
-    "    lon = np.hstack((lon,lon[:,0:1]+360.))\n",
-    "    if ni == 320:\n",
-    "        lon[367:,-1] = lon[367:,-1] - 360.\n",
-    "\n",
-    "    # Trick cartopy into doing the right thing:\n",
-    "    # it gets confused when the cyclic coords are identical\n",
-    "    lon[:,0] = lon[:,0]-1e-8\n",
-    "    \n",
-    "    # Periodicity\n",
-    "    lat  = np.concatenate((tlat,tlat),1)\n",
-    "    lat = lat[:,xL:xR]\n",
-    "    lat = np.hstack((lat,lat[:,0:1]))\n",
-    "\n",
-    "    field = np.ma.concatenate((field,field),1)\n",
-    "    field = field[:,xL:xR]\n",
-    "    field = np.ma.hstack((field,field[:,0:1]))\n",
-    "    return lon,lat,field"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "652bc60d-d17e-4bbb-bfce-2b323281f444",