Working with HDF5 files using SMAP data
The working directory was changed to E:/Univ of Utah Backup/Drive 4/G drive/NASA/SMAP/SMAP_Mar_April inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.Check what the file looks like
# print the file
print (h5_file)Class: H5File
Filename: E:\Univ of Utah Backup\Drive 4\G drive\NASA\SMAP\SMAP_Mar_April\SMAP_L3_SM_P_20150406_R14010_001.h5
Access type: H5F_ACC_RDWR
Listing:
name obj_type dataset.dims dataset.type_class
Metadata H5I_GROUP <NA> <NA>
Soil_Moisture_Retrieval_Data_AM H5I_GROUP <NA> <NA>
Soil_Moisture_Retrieval_Data_PM H5I_GROUP <NA> <NA># structure of the file
str(h5_file) Classes 'H5File', 'H5RefClass', 'R6' <H5File>
Inherits from: <H5RefClass>
Public:
attr_delete: function (attr_name)
attr_delete_by_idx: function (n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE,
attr_delete_by_name: function (attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)
attr_exists: function (attr_name)
attr_exists_by_name: function (attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)
attr_get_number: function ()
attr_info_by_idx: function (n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE,
attr_info_by_name: function (attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)
attr_name_by_idx: function (n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE,
attr_open: function (attr_name)
attr_open_by_idx: function (n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE,
attr_open_by_name: function (attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)
attr_rename: function (old_attr_name, new_attr_name)
attr_rename_by_name: function (old_attr_name, new_attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)
close: function ()
close_all: function (close_self = TRUE)
commit: function (name, dtype, link_create_pl = h5const$H5P_DEFAULT,
create_attr: function (attr_name, robj = NULL, dtype = NULL, space = NULL)
create_attr_by_name: function (attr_name, obj_name, robj = NULL, dtype = NULL, space = NULL,
create_dataset: function (name, robj = NULL, dtype = NULL, space = NULL, dims = NULL,
create_group: function (name, link_create_pl = h5const$H5P_DEFAULT, group_create_pl = h5const$H5P_DEFAULT,
create_reference: function (name = ".", space = NULL)
dec_ref: function ()
exists: function (name, link_access_pl = h5const$H5P_DEFAULT)
file_info: function ()
filename: E:\Univ of Utah Backup\Drive 4\G drive\NASA\SMAP\SMAP_Ma ...
flush: function (scope = h5const$H5F_SCOPE_GLOBAL)
get_file_id: function ()
get_filename: function ()
get_filesize: function ()
get_intent: function ()
get_obj_count: function (types = h5const$H5F_OBJ_ALL)
get_obj_ids: function (types = h5const$H5F_OBJ_ALL)
get_obj_name: function ()
get_obj_type: function ()
get_ref: function ()
group_info: function ()
group_info_by_idx: function (n, group_name = ".", index_field = h5const$H5_INDEX_NAME,
group_info_by_name: function (name, link_access_pl = h5const$H5P_DEFAULT)
id: active binding
id_env: active binding
inc_ref: function ()
initialize: function (filename = NULL, mode = c("a", "r", "r+", "w", "w-",
is_valid: active binding
link: function (obj, new_link_name, link_create_pl = h5const$H5P_DEFAULT,
link_copy_from: function (src_loc, src_name, dst_name, link_create_pl = h5const$H5P_DEFAULT,
link_copy_to: function (dst_loc, dst_name, src_name, link_create_pl = h5const$H5P_DEFAULT,
link_create_external: function (target_filename, target_obj_name, link_name, link_create_pl = h5const$H5P_DEFAULT,
link_create_hard: function (obj_loc, obj_name, link_name, link_create_pl = h5const$H5P_DEFAULT,
link_create_soft: function (target_path, link_name, link_create_pl = h5const$H5P_DEFAULT,
link_delete: function (name, link_access_pl = h5const$H5P_DEFAULT)
link_delete_by_idx: function (n, group_name = ".", index_field = h5const$H5_INDEX_NAME,
link_exists: function (name, link_access_pl = h5const$H5P_DEFAULT)
link_info: function (name, link_access_pl = h5const$H5P_DEFAULT)
link_info_by_idx: function (n, group_name = ".", index_field = h5const$H5_INDEX_NAME,
link_move_from: function (src_loc, src_name, dst_name, link_create_pl = h5const$H5P_DEFAULT,
link_move_to: function (dst_loc, dst_name, src_name, link_create_pl = h5const$H5P_DEFAULT,
link_name_by_idx: function (n, group_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE,
link_value: function (name, link_access_pl = h5const$H5P_DEFAULT)
link_value_by_idx: function (n, group_name = ".", index_field = h5const$H5_INDEX_NAME,
ls: function (recursive = FALSE, detailed = FALSE, index_type = h5const$H5_INDEX_NAME,
message: active binding
methods: function ()
mode: r+
mount: function (name, child)
names: active binding
obj_copy_from: function (src_loc, src_name, dst_name, object_copy_pl = h5const$H5P_DEFAULT,
obj_copy_to: function (dst_loc, dst_name, src_name, object_copy_pl = h5const$H5P_DEFAULT,
obj_info: function (remove_internal_use_only = TRUE)
obj_info_by_idx: function (n, group_name = ".", index_field = h5const$H5_INDEX_NAME,
obj_info_by_name: function (object_name, remove_internal_use_only = TRUE)
open: function (name, link_access_pl = h5const$H5P_DEFAULT, dataset_access_pl = h5const$H5P_DEFAULT,
open_by_idx: function (n, group_name = ".", index_type = h5const$H5_INDEX_NAME,
path_valid: function (path, check_object_valid = TRUE)
print: function (..., max.attributes = 10, max.listing = 10)
unmount: function (name)
Private:
closeFun: function (id)
pid: environment
pmessage:
stopOnInvalid: function (error.msg = "The object is invalid") List file data
h5_file$ls(recursive = TRUE) name link.type obj_type num_attrs group.nlinks
1 Metadata H5L_TYPE_HARD H5I_GROUP 4 11
2 Metadata/AcquisitionInformation H5L_TYPE_HARD H5I_GROUP 0 6
3 Metadata/AcquisitionInformation/platform H5L_TYPE_HARD H5I_GROUP 3 0
4 Metadata/AcquisitionInformation/radarDocument H5L_TYPE_HARD H5I_GROUP 3 0
5 Metadata/AcquisitionInformation/radiometerDocument H5L_TYPE_HARD H5I_GROUP 3 0
6 Metadata/AcquisitionInformation/radiometer H5L_TYPE_HARD H5I_GROUP 3 0
7 Metadata/AcquisitionInformation/radar H5L_TYPE_HARD H5I_GROUP 3 0
8 Metadata/AcquisitionInformation/platformDocument H5L_TYPE_HARD H5I_GROUP 3 0
9 Metadata/DataQuality H5L_TYPE_HARD H5I_GROUP 1 2
10 Metadata/DataQuality/DomainConsistency H5L_TYPE_HARD H5I_GROUP 5 0
11 Metadata/DataQuality/CompletenessOmission H5L_TYPE_HARD H5I_GROUP 5 0
12 Metadata/ProductSpecificationDocument H5L_TYPE_HARD H5I_GROUP 6 0
13 Metadata/SeriesIdentification H5L_TYPE_HARD H5I_GROUP 18 0
14 Metadata/DatasetIdentification H5L_TYPE_HARD H5I_GROUP 21 0
15 Metadata/Extent H5L_TYPE_HARD H5I_GROUP 7 0
16 Metadata/QADatasetIdentification H5L_TYPE_HARD H5I_GROUP 3 0
17 Metadata/GridSpatialRepresentation H5L_TYPE_HARD H5I_GROUP 6 4
18 Metadata/GridSpatialRepresentation/Row H5L_TYPE_HARD H5I_GROUP 2 0
19 Metadata/GridSpatialRepresentation/GridDefinitionDocument H5L_TYPE_HARD H5I_GROUP 3 0
20 Metadata/GridSpatialRepresentation/Column H5L_TYPE_HARD H5I_GROUP 2 0
21 Metadata/GridSpatialRepresentation/GridDefinition H5L_TYPE_HARD H5I_GROUP 2 0
22 Metadata/OrbitMeasuredLocation H5L_TYPE_HARD H5I_GROUP 2 0
23 Metadata/Lineage H5L_TYPE_HARD H5I_GROUP 0 6
24 Metadata/Lineage/InputConfiguration H5L_TYPE_HARD H5I_GROUP 4 0
25 Metadata/Lineage/EASEGRID_LON_M H5L_TYPE_HARD H5I_GROUP 4 0
26 Metadata/Lineage/L2_SM_P H5L_TYPE_HARD H5I_GROUP 6 0
27 Metadata/Lineage/MetadataConfiguration H5L_TYPE_HARD H5I_GROUP 4 0
28 Metadata/Lineage/OutputConfiguration H5L_TYPE_HARD H5I_GROUP 4 0
29 Metadata/Lineage/RunConfiguration H5L_TYPE_HARD H5I_GROUP 4 0
30 Metadata/ProcessStep H5L_TYPE_HARD H5I_GROUP 21 0
31 Soil_Moisture_Retrieval_Data_AM H5L_TYPE_HARD H5I_GROUP 0 31
32 Soil_Moisture_Retrieval_Data_AM/static_water_body_fraction H5L_TYPE_HARD H5I_DATASET 5 NA
33 Soil_Moisture_Retrieval_Data_AM/boresight_incidence H5L_TYPE_HARD H5I_DATASET 6 NA
34 Soil_Moisture_Retrieval_Data_AM/tb_time_utc H5L_TYPE_HARD H5I_DATASET 2 NA
35 Soil_Moisture_Retrieval_Data_AM/vegetation_opacity H5L_TYPE_HARD H5I_DATASET 5 NA
36 Soil_Moisture_Retrieval_Data_AM/tb_qual_flag_h H5L_TYPE_HARD H5I_DATASET 5 NA
37 Soil_Moisture_Retrieval_Data_AM/roughness_coefficient H5L_TYPE_HARD H5I_DATASET 5 NA
38 Soil_Moisture_Retrieval_Data_AM/landcover_class H5L_TYPE_HARD H5I_DATASET 3 NA
39 Soil_Moisture_Retrieval_Data_AM/EASE_row_index H5L_TYPE_HARD H5I_DATASET 5 NA
40 Soil_Moisture_Retrieval_Data_AM/tb_v_corrected H5L_TYPE_HARD H5I_DATASET 6 NA
41 Soil_Moisture_Retrieval_Data_AM/tb_4_corrected H5L_TYPE_HARD H5I_DATASET 6 NA
42 Soil_Moisture_Retrieval_Data_AM/longitude_centroid H5L_TYPE_HARD H5I_DATASET 6 NA
43 Soil_Moisture_Retrieval_Data_AM/longitude H5L_TYPE_HARD H5I_DATASET 2 NA
44 Soil_Moisture_Retrieval_Data_AM/landcover_class_fraction H5L_TYPE_HARD H5I_DATASET 5 NA
45 Soil_Moisture_Retrieval_Data_AM/latitude H5L_TYPE_HARD H5I_DATASET 2 NA
46 Soil_Moisture_Retrieval_Data_AM/retrieval_qual_flag H5L_TYPE_HARD H5I_DATASET 5 NA
47 Soil_Moisture_Retrieval_Data_AM/vegetation_water_content H5L_TYPE_HARD H5I_DATASET 6 NA
48 Soil_Moisture_Retrieval_Data_AM/soil_moisture H5L_TYPE_HARD H5I_DATASET 6 NA
49 Soil_Moisture_Retrieval_Data_AM/tb_3_corrected H5L_TYPE_HARD H5I_DATASET 6 NA
50 Soil_Moisture_Retrieval_Data_AM/tb_qual_flag_3 H5L_TYPE_HARD H5I_DATASET 5 NA
51 Soil_Moisture_Retrieval_Data_AM/tb_qual_flag_4 H5L_TYPE_HARD H5I_DATASET 5 NA
52 Soil_Moisture_Retrieval_Data_AM/tb_h_corrected H5L_TYPE_HARD H5I_DATASET 6 NA
53 Soil_Moisture_Retrieval_Data_AM/albedo H5L_TYPE_HARD H5I_DATASET 5 NA
54 Soil_Moisture_Retrieval_Data_AM/tb_time_seconds H5L_TYPE_HARD H5I_DATASET 6 NA
55 Soil_Moisture_Retrieval_Data_AM/soil_moisture_error H5L_TYPE_HARD H5I_DATASET 6 NA
56 Soil_Moisture_Retrieval_Data_AM/radar_water_body_fraction H5L_TYPE_HARD H5I_DATASET 5 NA
57 Soil_Moisture_Retrieval_Data_AM/tb_qual_flag_v H5L_TYPE_HARD H5I_DATASET 5 NA
58 Soil_Moisture_Retrieval_Data_AM/latitude_centroid H5L_TYPE_HARD H5I_DATASET 6 NA
59 Soil_Moisture_Retrieval_Data_AM/EASE_column_index H5L_TYPE_HARD H5I_DATASET 5 NA
60 Soil_Moisture_Retrieval_Data_AM/surface_temperature H5L_TYPE_HARD H5I_DATASET 6 NA
61 Soil_Moisture_Retrieval_Data_AM/freeze_thaw_fraction H5L_TYPE_HARD H5I_DATASET 5 NA
62 Soil_Moisture_Retrieval_Data_AM/surface_flag H5L_TYPE_HARD H5I_DATASET 5 NA
63 Soil_Moisture_Retrieval_Data_PM H5L_TYPE_HARD H5I_GROUP 0 31
64 Soil_Moisture_Retrieval_Data_PM/boresight_incidence_pm H5L_TYPE_HARD H5I_DATASET 6 NA
65 Soil_Moisture_Retrieval_Data_PM/EASE_row_index_pm H5L_TYPE_HARD H5I_DATASET 5 NA
66 Soil_Moisture_Retrieval_Data_PM/static_water_body_fraction_pm H5L_TYPE_HARD H5I_DATASET 5 NA
67 Soil_Moisture_Retrieval_Data_PM/freeze_thaw_fraction_pm H5L_TYPE_HARD H5I_DATASET 5 NA
68 Soil_Moisture_Retrieval_Data_PM/roughness_coefficient_pm H5L_TYPE_HARD H5I_DATASET 5 NA
69 Soil_Moisture_Retrieval_Data_PM/surface_flag_pm H5L_TYPE_HARD H5I_DATASET 5 NA
70 Soil_Moisture_Retrieval_Data_PM/retrieval_qual_flag_pm H5L_TYPE_HARD H5I_DATASET 5 NA
71 Soil_Moisture_Retrieval_Data_PM/tb_h_corrected_pm H5L_TYPE_HARD H5I_DATASET 6 NA
72 Soil_Moisture_Retrieval_Data_PM/soil_moisture_pm H5L_TYPE_HARD H5I_DATASET 6 NA
73 Soil_Moisture_Retrieval_Data_PM/tb_qual_flag_4_pm H5L_TYPE_HARD H5I_DATASET 5 NA
74 Soil_Moisture_Retrieval_Data_PM/tb_3_corrected_pm H5L_TYPE_HARD H5I_DATASET 6 NA
75 Soil_Moisture_Retrieval_Data_PM/tb_qual_flag_h_pm H5L_TYPE_HARD H5I_DATASET 5 NA
76 Soil_Moisture_Retrieval_Data_PM/latitude_centroid_pm H5L_TYPE_HARD H5I_DATASET 6 NA
77 Soil_Moisture_Retrieval_Data_PM/EASE_column_index_pm H5L_TYPE_HARD H5I_DATASET 5 NA
78 Soil_Moisture_Retrieval_Data_PM/tb_time_seconds_pm H5L_TYPE_HARD H5I_DATASET 6 NA
79 Soil_Moisture_Retrieval_Data_PM/tb_4_corrected_pm H5L_TYPE_HARD H5I_DATASET 6 NA
80 Soil_Moisture_Retrieval_Data_PM/soil_moisture_error_pm H5L_TYPE_HARD H5I_DATASET 6 NA
81 Soil_Moisture_Retrieval_Data_PM/landcover_class_pm H5L_TYPE_HARD H5I_DATASET 3 NA
82 Soil_Moisture_Retrieval_Data_PM/tb_time_utc_pm H5L_TYPE_HARD H5I_DATASET 2 NA
83 Soil_Moisture_Retrieval_Data_PM/longitude_pm H5L_TYPE_HARD H5I_DATASET 6 NA
group.mounted dataset.rank dataset.dims dataset.maxdims dataset.type_class dataset.space_class committed_type
1 0 NA <NA> <NA> <NA> <NA> <NA>
2 0 NA <NA> <NA> <NA> <NA> <NA>
3 0 NA <NA> <NA> <NA> <NA> <NA>
4 0 NA <NA> <NA> <NA> <NA> <NA>
5 0 NA <NA> <NA> <NA> <NA> <NA>
6 0 NA <NA> <NA> <NA> <NA> <NA>
7 0 NA <NA> <NA> <NA> <NA> <NA>
8 0 NA <NA> <NA> <NA> <NA> <NA>
9 0 NA <NA> <NA> <NA> <NA> <NA>
10 0 NA <NA> <NA> <NA> <NA> <NA>
11 0 NA <NA> <NA> <NA> <NA> <NA>
12 0 NA <NA> <NA> <NA> <NA> <NA>
13 0 NA <NA> <NA> <NA> <NA> <NA>
14 0 NA <NA> <NA> <NA> <NA> <NA>
15 0 NA <NA> <NA> <NA> <NA> <NA>
16 0 NA <NA> <NA> <NA> <NA> <NA>
17 0 NA <NA> <NA> <NA> <NA> <NA>
18 0 NA <NA> <NA> <NA> <NA> <NA>
19 0 NA <NA> <NA> <NA> <NA> <NA>
20 0 NA <NA> <NA> <NA> <NA> <NA>
21 0 NA <NA> <NA> <NA> <NA> <NA>
22 0 NA <NA> <NA> <NA> <NA> <NA>
23 0 NA <NA> <NA> <NA> <NA> <NA>
24 0 NA <NA> <NA> <NA> <NA> <NA>
25 0 NA <NA> <NA> <NA> <NA> <NA>
26 0 NA <NA> <NA> <NA> <NA> <NA>
27 0 NA <NA> <NA> <NA> <NA> <NA>
28 0 NA <NA> <NA> <NA> <NA> <NA>
29 0 NA <NA> <NA> <NA> <NA> <NA>
30 0 NA <NA> <NA> <NA> <NA> <NA>
31 0 NA <NA> <NA> <NA> <NA> <NA>
32 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
33 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
34 NA 2 964 x 406 964 x 406 H5T_STRING H5S_SIMPLE <NA>
35 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
36 NA 2 964 x 406 964 x 406 H5T_INTEGER H5S_SIMPLE <NA>
37 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
38 NA 3 3 x 964 x 406 3 x 964 x 406 H5T_INTEGER H5S_SIMPLE <NA>
39 NA 2 964 x 406 964 x 406 H5T_INTEGER H5S_SIMPLE <NA>
40 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
41 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
42 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
43 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
44 NA 3 3 x 964 x 406 3 x 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
45 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
46 NA 2 964 x 406 964 x 406 H5T_INTEGER H5S_SIMPLE <NA>
47 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
48 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
49 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
50 NA 2 964 x 406 964 x 406 H5T_INTEGER H5S_SIMPLE <NA>
51 NA 2 964 x 406 964 x 406 H5T_INTEGER H5S_SIMPLE <NA>
52 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
53 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
54 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
55 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
56 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
57 NA 2 964 x 406 964 x 406 H5T_INTEGER H5S_SIMPLE <NA>
58 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
59 NA 2 964 x 406 964 x 406 H5T_INTEGER H5S_SIMPLE <NA>
60 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
61 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
62 NA 2 964 x 406 964 x 406 H5T_INTEGER H5S_SIMPLE <NA>
63 0 NA <NA> <NA> <NA> <NA> <NA>
64 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
65 NA 2 964 x 406 964 x 406 H5T_INTEGER H5S_SIMPLE <NA>
66 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
67 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
68 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
69 NA 2 964 x 406 964 x 406 H5T_INTEGER H5S_SIMPLE <NA>
70 NA 2 964 x 406 964 x 406 H5T_INTEGER H5S_SIMPLE <NA>
71 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
72 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
73 NA 2 964 x 406 964 x 406 H5T_INTEGER H5S_SIMPLE <NA>
74 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
75 NA 2 964 x 406 964 x 406 H5T_INTEGER H5S_SIMPLE <NA>
76 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
77 NA 2 964 x 406 964 x 406 H5T_INTEGER H5S_SIMPLE <NA>
78 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
79 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
80 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
81 NA 3 3 x 964 x 406 3 x 964 x 406 H5T_INTEGER H5S_SIMPLE <NA>
82 NA 2 964 x 406 964 x 406 H5T_STRING H5S_SIMPLE <NA>
83 NA 2 964 x 406 964 x 406 H5T_FLOAT H5S_SIMPLE <NA>
[ reached 'max' / getOption("max.print") -- omitted 11 rows ]lat_pm = h5_file[["Soil_Moisture_Retrieval_Data_PM/latitude_pm"]]
lon_pm = h5_file[["Soil_Moisture_Retrieval_Data_PM/longitude_pm"]]
soil_mois = h5_file[["Soil_Moisture_Retrieval_Data_PM/soil_moisture_pm"]]
h5attributes(lat_pm)$long_name
[1] "Latitude of the center of the Earth based grid cell."
$coordinates
[1] "/Soil_Moisture_Retrieval_Data_AM/latitude /Soil_Moisture_Retrieval_Data_AM/longitude"
$valid_min
[1] -90
$valid_max
[1] 90
$`_FillValue`
[1] -9999
$units
[1] "degrees_north"h5attributes(lon_pm)$long_name
[1] "Longitude of the center of the Earth based grid cell."
$units
[1] "degrees_east"
$coordinates
[1] "/Soil_Moisture_Retrieval_Data_AM/latitude /Soil_Moisture_Retrieval_Data_AM/longitude"
$valid_min
[1] -180
$valid_max
[1] 179.999
$`_FillValue`
[1] -9999h5attributes(soil_mois)$long_name
[1] "Representative soil moisture measurement for the Earth based grid cell."
$units
[1] "cm**3/cm**3"
$coordinates
[1] "/Soil_Moisture_Retrieval_Data_AM/latitude /Soil_Moisture_Retrieval_Data_AM/longitude"
$valid_min
[1] 0.02
$valid_max
[1] 0.5
$`_FillValue`
[1] -9999h5attr_names(lon_pm)[1] "long_name" "units" "coordinates" "valid_min" "valid_max" "_FillValue" h5attr_names(soil_mois)[1] "long_name" "units" "coordinates" "valid_min" "valid_max" "_FillValue" Start extraction of Lat, Long and Data to plot PM data
lat_pm # Check the number of dimensionsClass: H5D
Dataset: /Soil_Moisture_Retrieval_Data_PM/latitude_pm
Filename: E:\Univ of Utah Backup\Drive 4\G drive\NASA\SMAP\SMAP_Mar_April\SMAP_L3_SM_P_20150406_R14010_001.h5
Access type: H5F_ACC_RDWR
Attributes: long_name, coordinates, valid_min, valid_max, _FillValue, units
Datatype: H5T_IEEE_F32LE
Space: Type=Simple Dims=964 x 406 Maxdims=964 x 406
Chunk: 964 x 1lats = lat_pm[,] #From the dimension above, put the 2D data into this variable
lats[lats==-9999.0] = NA
lats = colMeans(lats,na.rm=T)
lats[is.nan(lats)] = NA
lats = na.approx(lats)
lats = sort(lats)
lon_pmClass: H5D
Dataset: /Soil_Moisture_Retrieval_Data_PM/longitude_pm
Filename: E:\Univ of Utah Backup\Drive 4\G drive\NASA\SMAP\SMAP_Mar_April\SMAP_L3_SM_P_20150406_R14010_001.h5
Access type: H5F_ACC_RDWR
Attributes: long_name, units, coordinates, valid_min, valid_max, _FillValue
Datatype: H5T_IEEE_F32LE
Space: Type=Simple Dims=964 x 406 Maxdims=964 x 406
Chunk: 964 x 1lons = lon_pm[,]
lons[lons==-9999.0] = NA
lons = (rowMeans(lons,na.rm=T))
lons[is.nan(lons)] = NA
lons = na.approx(lons)
soil_moisClass: H5D
Dataset: /Soil_Moisture_Retrieval_Data_PM/soil_moisture_pm
Filename: E:\Univ of Utah Backup\Drive 4\G drive\NASA\SMAP\SMAP_Mar_April\SMAP_L3_SM_P_20150406_R14010_001.h5
Access type: H5F_ACC_RDWR
Attributes: long_name, units, coordinates, valid_min, valid_max, _FillValue
Datatype: H5T_IEEE_F32LE
Space: Type=Simple Dims=964 x 406 Maxdims=964 x 406
Chunk: 964 x 1sms = soil_mois[,]
sms[sms==-9999.0] = NA
rotate <- function(x) t(apply(x, 2, rev))
image.plot(lons, lats, (rotate(t(sms))))
map(add=T, col = "lightgray", main = "Evening (PM)")
AM data plot
lat_am = h5_file[["Soil_Moisture_Retrieval_Data_AM/latitude"]]
lon_am = h5_file[["Soil_Moisture_Retrieval_Data_AM/longitude"]]
soil_mois = h5_file[["Soil_Moisture_Retrieval_Data_AM/soil_moisture"]]
lat_am # Check the number of dimensionsClass: H5D
Dataset: /Soil_Moisture_Retrieval_Data_AM/latitude
Filename: E:\Univ of Utah Backup\Drive 4\G drive\NASA\SMAP\SMAP_Mar_April\SMAP_L3_SM_P_20150406_R14010_001.h5
Access type: H5F_ACC_RDWR
Attributes: long_name, units
Datatype: H5T_IEEE_F32LE
Space: Type=Simple Dims=964 x 406 Maxdims=964 x 406
Chunk: 964 x 1lats = lat_am[,] #From the dimension above, put the 2D data into this variable
lats[lats==-9999.0] = NA
lats = colMeans(lats,na.rm=T)
lats[is.nan(lats)] = NA
lats = na.approx(lats)
lats = sort(lats)
lon_amClass: H5D
Dataset: /Soil_Moisture_Retrieval_Data_AM/longitude
Filename: E:\Univ of Utah Backup\Drive 4\G drive\NASA\SMAP\SMAP_Mar_April\SMAP_L3_SM_P_20150406_R14010_001.h5
Access type: H5F_ACC_RDWR
Attributes: long_name, units
Datatype: H5T_IEEE_F32LE
Space: Type=Simple Dims=964 x 406 Maxdims=964 x 406
Chunk: 964 x 1lons = lon_am[,]
lons[lons==-9999.0] = NA
lons = (rowMeans(lons,na.rm=T))
lons[is.nan(lons)] = NA
lons = na.approx(lons)
soil_moisClass: H5D
Dataset: /Soil_Moisture_Retrieval_Data_AM/soil_moisture
Filename: E:\Univ of Utah Backup\Drive 4\G drive\NASA\SMAP\SMAP_Mar_April\SMAP_L3_SM_P_20150406_R14010_001.h5
Access type: H5F_ACC_RDWR
Attributes: long_name, units, coordinates, valid_min, valid_max, _FillValue
Datatype: H5T_IEEE_F32LE
Space: Type=Simple Dims=964 x 406 Maxdims=964 x 406
Chunk: 964 x 1sms = soil_mois[,]
sms[sms==-9999.0] = NA
rotate <- function(x) t(apply(x, 2, rev))
image.plot(lons, lats, (rotate(t(sms))))
map(add=T, col = "lightgray")
h5close(h5_file)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