diff --git a/coordinator/EnvSuitPipeline.py b/coordinator/EnvSuitPipeline.py
index 80d160f1ab4dfc3ea75bc8f95936648f054263c9..f790a1032236d1d9cd64576d0917ac52b530c51e 100644
--- a/coordinator/EnvSuitPipeline.py
+++ b/coordinator/EnvSuitPipeline.py
@@ -165,23 +165,6 @@ def run_pipeline(pipeline_config, region, dateString, extracted = False, prevent
     region_outPath = os.path.join(outPath,'ENVIRONMENT_2.0_'+dateString,'processed',region)
     if prevent_overwrite: assert not os.path.exists(region_outPath)
 
-    # Get spatial points file for the region. The file template can be specified in the config.
-    if "SPATIAL_POINTS_FILE_TEMPLATE" in pipeline_config:
-        region_spatial_points_file_template = pipeline_config["SPATIAL_POINTS_FILE_TEMPLATE"]
-        region_spatial_points_file = Template(region_spatial_points_file_template).substitute(Region=region)
-    else:
-        region_spatial_points_file = resourcesPath + 'assets/' + 'input_spatial_points_' + region + '.csv'
-
-    input_spatial_points_file = workPath + 'input_spatial_points.csv'
-    if prevent_overwrite: assert not os.path.exists(input_spatial_points_file)
-    shutil.copy(region_spatial_points_file,input_spatial_points_file)
-    """
-    read in the input_spatial_points.csv file and get the number of spatial points which are marked as landpoint=True
-    (we will be finltering the non-landpoint locations)
-    """
-    spatial_points = pd.read_csv(input_spatial_points_file)
-    spatial_dim = spatial_points[spatial_points['landpoint']].shape[0]
-
     # Generate extraction (input) and output temporal points files
     timeresolution = 3 # hours
 
@@ -207,7 +190,7 @@ def run_pipeline(pipeline_config, region, dateString, extracted = False, prevent
     # Modify run_config
     config[ParamsFileParser.TIMEPOINTS_FILE_KEY] = extraction_temporal_points_file
     config[ParamsFileParser.OUTPUT_DIR_KEY] = workPath
-    config[ParamsFileParser.SPATIAL_POINTS_FILE_KEY] = input_spatial_points_file
+    # config[ParamsFileParser.SPATIAL_POINTS_FILE_KEY] = input_spatial_points_file
     # note that this field will only get used by the ewa5_met_data_extraction code, which uses a multi-processor module
     config[ParamsFileParser.MAX_PROCESSORS_KEY] = MAX_WORKERS
 
@@ -286,6 +269,15 @@ def run_pipeline(pipeline_config, region, dateString, extracted = False, prevent
                 result = pd.read_csv(resultFile)
                 result_dims = result.shape
 
+                """
+                read in the input_spatial_points.csv file and get the number of spatial points - this is used for 
+                sense-checking the dimensions of the output
+                """
+                # todo we could swap the spatial points file for a file specifying the expected dimensions - much smaller
+                region_spatial_points_file = resourcesPath + 'assets/' + 'input_spatial_points_' + region + '.csv'
+                spatial_points = pd.read_csv(region_spatial_points_file)
+                spatial_dim = spatial_points.shape[0]
+
                 if ((result_dims[0] != spatial_dim) or (result_dims[1] != (temporal_dim + 4))): # + 4 required because there are extra columns in the result file
                     logger.error(f"Result dimension {result_dims} does not match with the expected: ({spatial_dim}, {temporal_dim + 4})")
                     raise IndexError
diff --git a/docs/_source/deployment_notes.rst b/docs/_source/deployment_notes.rst
new file mode 100644
index 0000000000000000000000000000000000000000..2b6ed94148ff6ec6ff92de40297b6131ff6a6f76
--- /dev/null
+++ b/docs/_source/deployment_notes.rst
@@ -0,0 +1,111 @@
+
+.. _deployment_notes:
+
+Deployment notes
+================
+
+The EWS pipeline uses an input grid to specify the points to be included in the calculations. The grid is determined by
+the UK Met Office (UKMO). The points specified within the NAME and weather data provided by the UKMO must be matched by
+the landpoint files specified below. The system used by the EWS uses a series of masks, to specify which points are over
+water, or outside country boundaries. The masking system allows faster calculation (avoiding areas that are not relevant)
+and plotting that only shows the regions of interest. The spatial grids used by the EWS pipeline must match the
+UKMO grid in number of points and sort order:
+
+.. code-block:: python
+
+    landpoint_df.sort_values(['longitude', 'latitude'], ascending = [True, True])
+
+The precision of the longitude and latitude values is not important, provided any differences in precision do not affect
+the sort order.
+
+Filtering is achieved using a column specifying whether it is "included" or not:
+
+.. code-block::
+
+    longitude,latitude,included
+    21.445310,-5.015625,True
+    21.445310,-4.921875,False
+    21.445310,-4.828125,True
+    21.445310,-4.734375,True
+
+The longitude and latitude areas are not technically necessary,
+as filtering is performed by building a series of true/false values to filter the incoming dataframe (hence the
+importance of the sort order and row count).
+
+.. code-block:: python
+
+    spatial_points_df = pd.read_csv(landpoint_file_path)
+    rows_to_keep = spatial_points_df['included']
+    filtered_df = unfiltered_df[rows_to_keep]
+
+
+Location of grid files
+======================
+
+Met extractor
+-------------
+
+The main input grid is stored in the assets folder of the met_extractor resources. e.g.
+
+**regions/<EastAfrica-SouthAsia>/met_extractor/assets/input_spatial_points_<EastAfrica-SouthAsia>.csv**
+
+.. admonition:: Configuration files from Cambridge required
+
+    This grid file is not used for masking, it is used for sense-checking the dimensions of output data. We could replace it
+    with the expected dimensions and extent of the input/output data.
+
+The file path is built within the code, so it must conform to the format:
+
+.. code-block:: python
+
+    'input_spatial_points_' + region + '.csv'
+
+
+('region' is specified in the JSON config, e.g. config_EastAfrica_fc_live.json:
+
+.. code-block:: json
+
+    "RegionName" : "EastAfrica"
+
+Post processing
+---------------
+
+edit the "COUNTRY_LANDPOINTS_FILE" field in the chart config files used for post-processing e.g.
+
+regions/EastAfrica/resources/plotting/configs/chart/CHART_CONFIG_ETHIOPIA_PINE.json
+
+to use a grid that masks the points outside the country boundaries, stored in:
+
+/regions/EastAfrica/resources/plotting/assets/gis_data/<country>/<country>_points.txt
+
+The post-processing mask files are used in:
+
+:func:`ews_postprocessing.utils.processing_utils.mask_dataframe_for_landfile`
+
+this function is called from the Deposition, Environmental suitability and Epidemology pipelines to filter for country boundaries.
+
+Deposition: :meth:`~ews_postprocessing.deposition.condense_deposition_csvs.ConvertCondenseAndNormalizeDepositionCSV.mask_csv_for_land`
+
+Environmental suitability: :meth:`~ews_postprocessing.environmental_suitability.condense_environment_csvs.CondenseEnvSuitCSV.process`
+
+Epidemiology: :meth:`~ews_postprocessing.epi.epi_post_processor.EPIPostPostProcessor._mask_epi_csvs`
+
+
+Creating the grid files
+=======================
+
+A utility script:
+
+ews_postprocessing/utils/filter_country_points.py
+
+Can be used to create a set of mask tiles. It takes an ncdf file (provided by the UKMO) and writes a sorted list of lat
+lon values, with an "included" column, set to True where the point is within the shape file of interest.
+
+Defining the Met Data cube files
+================================
+
+edit "MET_DATA_TYPE": "NAME", field in the /regions/EastAfrica/resources/met_extractor/configs/template_operational_config.json file to match the correct met data lookup specified in:
+
+regions/EastAfrica/resources/met_extractor/configs/FIELD_NAME_CONSTANTS.csv
+
+this ensures the correct Met nc files are located
diff --git a/docs/_source/installation.rst b/docs/_source/installation.rst
index 98779016115c1fb6595030d876264a46fc17397a..31dec89cb2e4237db3559f13bd387eb1e784d872 100644
--- a/docs/_source/installation.rst
+++ b/docs/_source/installation.rst
@@ -8,6 +8,8 @@ UK Met Office. These instructions will allow you to get the EWS system running o
 data from the UK Met office (both weather data and the output of NAME runs. The Cambridge team can provide you with the
 required configuration files and project assets for the regions currently being monitored.
 
+See also :ref:`deployment notes <deployment_notes>`
+
 The example code below is from a Linux system using the Bash shell.
 
 1: Create installation dirs:
diff --git a/docs/api.rst b/docs/api.rst
index 3d57073301b307ffbeb4f08da253caf2ac081c6f..92c6af18c4618c7a5de60e983a8304f22acc9f17 100644
--- a/docs/api.rst
+++ b/docs/api.rst
@@ -6,7 +6,7 @@ API
    :template: custom-module-template.rst
    :recursive:
 
-..    coordinator
+    coordinator
     plotting
     ews_postprocessing
     met_processing
diff --git a/tests/test_data/test_deployment/regions/EastAfrica/resources/met_extractor/assets/input_spatial_points_EastAfrica.csv b/tests/test_data/test_deployment/regions/EastAfrica/resources/met_extractor/assets/input_spatial_points_EastAfrica.csv
index b9136ae82987a0c25da60b6550245c3ab3a51dcc..ff5d243942ac3b6c159e7599905d7214c59a0025 100644
--- a/tests/test_data/test_deployment/regions/EastAfrica/resources/met_extractor/assets/input_spatial_points_EastAfrica.csv
+++ b/tests/test_data/test_deployment/regions/EastAfrica/resources/met_extractor/assets/input_spatial_points_EastAfrica.csv
@@ -1,127 +1,127 @@
-longitude,latitude,landpoint
-38.60156,8.109375,True
-38.60156,8.203125,True
-38.60156,8.296875,True
-38.60156,8.390625,True
-38.60156,8.484375,True
-38.60156,8.578125,True
-38.60156,8.671875,True
-38.60156,8.765625,True
-38.60156,8.859375,True
-38.742185,8.109375,True
-38.742185,8.203125,True
-38.742185,8.296875,True
-38.742185,8.390625,True
-38.742185,8.484375,True
-38.742185,8.578125,True
-38.742185,8.671875,True
-38.742185,8.765625,True
-38.742185,8.859375,True
-38.88281,8.109375,True
-38.88281,8.203125,True
-38.88281,8.296875,True
-38.88281,8.390625,True
-38.88281,8.484375,True
-38.88281,8.578125,True
-38.88281,8.671875,True
-38.88281,8.765625,True
-38.88281,8.859375,True
-39.023435,8.109375,True
-39.023435,8.203125,True
-39.023435,8.296875,True
-39.023435,8.390625,True
-39.023435,8.484375,True
-39.023435,8.578125,True
-39.023435,8.671875,True
-39.023435,8.765625,True
-39.023435,8.859375,True
-39.16406,8.109375,True
-39.16406,8.203125,True
-39.16406,8.296875,True
-39.16406,8.390625,True
-39.16406,8.484375,True
-39.16406,8.578125,True
-39.16406,8.671875,True
-39.16406,8.765625,True
-39.16406,8.859375,True
-39.304685,8.109375,True
-39.304685,8.203125,True
-39.304685,8.296875,True
-39.304685,8.390625,True
-39.304685,8.484375,True
-39.304685,8.578125,True
-39.304685,8.671875,True
-39.304685,8.765625,True
-39.304685,8.859375,True
-39.44531,8.109375,True
-39.44531,8.203125,True
-39.44531,8.296875,True
-39.44531,8.390625,True
-39.44531,8.484375,True
-39.44531,8.578125,True
-39.44531,8.671875,True
-39.44531,8.765625,True
-39.44531,8.859375,True
-39.585935,8.109375,True
-39.585935,8.203125,True
-39.585935,8.296875,True
-39.585935,8.390625,True
-39.585935,8.484375,True
-39.585935,8.578125,True
-39.585935,8.671875,True
-39.585935,8.765625,True
-39.585935,8.859375,True
-39.72656,8.109375,True
-39.72656,8.203125,True
-39.72656,8.296875,True
-39.72656,8.390625,True
-39.72656,8.484375,True
-39.72656,8.578125,True
-39.72656,8.671875,True
-39.72656,8.765625,True
-39.72656,8.859375,True
-39.867185,8.109375,True
-39.867185,8.203125,True
-39.867185,8.296875,True
-39.867185,8.390625,True
-39.867185,8.484375,True
-39.867185,8.578125,True
-39.867185,8.671875,True
-39.867185,8.765625,True
-39.867185,8.859375,True
-40.00781,8.109375,True
-40.00781,8.203125,True
-40.00781,8.296875,True
-40.00781,8.390625,True
-40.00781,8.484375,True
-40.00781,8.578125,True
-40.00781,8.671875,True
-40.00781,8.765625,True
-40.00781,8.859375,True
-40.148435,8.109375,True
-40.148435,8.203125,True
-40.148435,8.296875,True
-40.148435,8.390625,True
-40.148435,8.484375,True
-40.148435,8.578125,True
-40.148435,8.671875,True
-40.148435,8.765625,True
-40.148435,8.859375,True
-40.28906,8.109375,True
-40.28906,8.203125,True
-40.28906,8.296875,True
-40.28906,8.390625,True
-40.28906,8.484375,True
-40.28906,8.578125,True
-40.28906,8.671875,True
-40.28906,8.765625,True
-40.28906,8.859375,True
-40.429685,8.109375,True
-40.429685,8.203125,True
-40.429685,8.296875,True
-40.429685,8.390625,True
-40.429685,8.484375,True
-40.429685,8.578125,True
-40.429685,8.671875,True
-40.429685,8.765625,True
-40.429685,8.859375,True
+longitude,latitude
+38.60156,8.109375
+38.60156,8.203125
+38.60156,8.296875
+38.60156,8.390625
+38.60156,8.484375
+38.60156,8.578125
+38.60156,8.671875
+38.60156,8.765625
+38.60156,8.859375
+38.742185,8.109375
+38.742185,8.203125
+38.742185,8.296875
+38.742185,8.390625
+38.742185,8.484375
+38.742185,8.578125
+38.742185,8.671875
+38.742185,8.765625
+38.742185,8.859375
+38.88281,8.109375
+38.88281,8.203125
+38.88281,8.296875
+38.88281,8.390625
+38.88281,8.484375
+38.88281,8.578125
+38.88281,8.671875
+38.88281,8.765625
+38.88281,8.859375
+39.023435,8.109375
+39.023435,8.203125
+39.023435,8.296875
+39.023435,8.390625
+39.023435,8.484375
+39.023435,8.578125
+39.023435,8.671875
+39.023435,8.765625
+39.023435,8.859375
+39.16406,8.109375
+39.16406,8.203125
+39.16406,8.296875
+39.16406,8.390625
+39.16406,8.484375
+39.16406,8.578125
+39.16406,8.671875
+39.16406,8.765625
+39.16406,8.859375
+39.304685,8.109375
+39.304685,8.203125
+39.304685,8.296875
+39.304685,8.390625
+39.304685,8.484375
+39.304685,8.578125
+39.304685,8.671875
+39.304685,8.765625
+39.304685,8.859375
+39.44531,8.109375
+39.44531,8.203125
+39.44531,8.296875
+39.44531,8.390625
+39.44531,8.484375
+39.44531,8.578125
+39.44531,8.671875
+39.44531,8.765625
+39.44531,8.859375
+39.585935,8.109375
+39.585935,8.203125
+39.585935,8.296875
+39.585935,8.390625
+39.585935,8.484375
+39.585935,8.578125
+39.585935,8.671875
+39.585935,8.765625
+39.585935,8.859375
+39.72656,8.109375
+39.72656,8.203125
+39.72656,8.296875
+39.72656,8.390625
+39.72656,8.484375
+39.72656,8.578125
+39.72656,8.671875
+39.72656,8.765625
+39.72656,8.859375
+39.867185,8.109375
+39.867185,8.203125
+39.867185,8.296875
+39.867185,8.390625
+39.867185,8.484375
+39.867185,8.578125
+39.867185,8.671875
+39.867185,8.765625
+39.867185,8.859375
+40.00781,8.109375
+40.00781,8.203125
+40.00781,8.296875
+40.00781,8.390625
+40.00781,8.484375
+40.00781,8.578125
+40.00781,8.671875
+40.00781,8.765625
+40.00781,8.859375
+40.148435,8.109375
+40.148435,8.203125
+40.148435,8.296875
+40.148435,8.390625
+40.148435,8.484375
+40.148435,8.578125
+40.148435,8.671875
+40.148435,8.765625
+40.148435,8.859375
+40.28906,8.109375
+40.28906,8.203125
+40.28906,8.296875
+40.28906,8.390625
+40.28906,8.484375
+40.28906,8.578125
+40.28906,8.671875
+40.28906,8.765625
+40.28906,8.859375
+40.429685,8.109375
+40.429685,8.203125
+40.429685,8.296875
+40.429685,8.390625
+40.429685,8.484375
+40.429685,8.578125
+40.429685,8.671875
+40.429685,8.765625
+40.429685,8.859375
diff --git a/tests/test_data/test_deployment/regions/EastAfrica/resources/plotting/assets/gis_data/east_africa/small_east_africa_points.txt b/tests/test_data/test_deployment/regions/EastAfrica/resources/plotting/assets/gis_data/east_africa/small_east_africa_points.txt
index b9136ae82987a0c25da60b6550245c3ab3a51dcc..720925fa5f947655efc3b3b09bc7daca4dce9b06 100644
--- a/tests/test_data/test_deployment/regions/EastAfrica/resources/plotting/assets/gis_data/east_africa/small_east_africa_points.txt
+++ b/tests/test_data/test_deployment/regions/EastAfrica/resources/plotting/assets/gis_data/east_africa/small_east_africa_points.txt
@@ -1,4 +1,4 @@
-longitude,latitude,landpoint
+longitude,latitude,included
 38.60156,8.109375,True
 38.60156,8.203125,True
 38.60156,8.296875,True
diff --git a/tests/test_data/test_deployment/regions/EastAfrica/resources/plotting/assets/gis_data/ethiopia/small_ethiopia_points.txt b/tests/test_data/test_deployment/regions/EastAfrica/resources/plotting/assets/gis_data/ethiopia/small_ethiopia_points.txt
index 040c41b752564eb6e89cf53dbe0733cfda7543ba..8282fd5da2b794fad1b177a0874525e6b028a4f1 100644
--- a/tests/test_data/test_deployment/regions/EastAfrica/resources/plotting/assets/gis_data/ethiopia/small_ethiopia_points.txt
+++ b/tests/test_data/test_deployment/regions/EastAfrica/resources/plotting/assets/gis_data/ethiopia/small_ethiopia_points.txt
@@ -1,4 +1,4 @@
-longitude,latitude,landpoint
+longitude,latitude,included
 38.60156,8.109375,True
 38.60156,8.203125,True
 38.60156,8.296875,True