imports.gocad package

Submodules

imports.gocad.gocad_filestr_types module

class imports.gocad.gocad_filestr_types.GocadFileDataStrMap

Bases: lib.imports.data_str_types.FileDataStructMap

GOCAD_HEADERS = {'GP': ['GOCAD HETEROGENEOUSGROUP 1', 'GOCAD HOMOGENEOUSGROUP 1'], 'PL': ['GOCAD PLINE 1'], 'SG': ['GOCAD SGRID 1'], 'TS': ['GOCAD TSURF 1'], 'VO': ['GOCAD VOXET 1'], 'VS': ['GOCAD VSET 1'], 'WL': ['GOCAD WELL 1']}

Constant assigns possible headers to each filename extension

_GocadFileDataStrMap__get_ext(filename_str)

is_borehole(filename_str)

Routine to recognise a borehole file

Parameters:filename_str – filename (including path) of GOCAD object file Returns:True if this file contains a borehole data structure

is_flat_shape(filename_str)

Routine to recognise a flat shape file e.g. triangles, planes in 3d

Parameters:filename_str – filename (including path) of GOCAD object file Returns:True if this file contains a flat shape data structure

is_mixture(filename_str)

Routine to recognise a file with a mixture of data structures

Parameters:filename_str – filename (including path) of GOCAD object file Returns:True if this file contains a mixture of data structures

is_points(filename_str)

Routine to recognise a points file

Parameters:filename_str – filename (including path) of GOCAD object file Returns:True if this file contains a points data structure

is_volume(filename_str)

Routine to recognise a volume file

Parameters:filename_str – filename (including path) of GOCAD object file Returns:True if this file contains a volume data structure

imports.gocad.gocad_importer module

This contains the GocadImporter class, which is the main class used for parsing GOCAD object files. It also contains other functions for parsing GOCAD group files.

class imports.gocad.gocad_importer.GocadImporter(debug_level, base_xyz=(0.0, 0.0, 0.0), group_name='', nondefault_coords=False, stop_on_exc=True, ct_file_dict={})

Bases: object

Class used to read GOCAD files and store their details

Initialise class

Parameters:

• debug_level – debug level taken from ‘logging’ module e.g. logging.DEBUG
• base_xyz – optional (x,y,z) floating point tuple, base_xyz is added to all coordinates before they are output, default is (0.0, 0.0, 0.0)
• group_name – optional string, name of group if this gocad file is within a group, default is “”
• nondefault_coords – optional flag, supports non-default coordinates, default is False
• ct_file_dict – a dictionary of files which contain a tuple: (filename of CSV colour table, list of values to be rendered transparent) key is GOCAD filename

COORD_OFFSETS = {'FROM_SHAPE': (535100.0, 0.0, 0.0)}

Coordinate offsets, when file contains a coordinate system that is not “DEFAULT” The named coordinate system and (X,Y,Z) offset will apply

SKIP_FLAGS_FILE = True

Don’t read flags file

SUPPORTED_EXTS = ['TS', 'VS', 'PL', 'GP', 'VO', 'WL', 'SG']

List of file extensions to search for

WELL_LINE_WIDTH = 10

Line width for drawing wells

_GocadImporter__init_geometry(geom_obj, local_prop_idx_list=None, prop_idx=None)

Convert GocadImporter to MODEL_GEOMETRY version

Parameters:

• geom_obj – MODEL_GEOMETRY object where GocadImporter data is placed
• local_prop_idx_list – optional, if set, then will place multiple local property data values in object
• prop_idx – optional, if set, then will place property data in object

_GocadImporter__init_metadata(meta_obj, local_prop_idx_list=None, prop_idx=None)

Extract metadata from GocadImporter and place in metadata object

Parameters:

• meta_obj – metadata object which will hold data from GocadImporter object
• local_prop_idx_list – optional, if set, then will place multiple local property data values in object
• prop_idx – optional, if set, then will place property data in object

_GocadImporter__init_style(style_obj, local_prop_idx_list=None, prop_idx=None)

Extract style data from GocadImporter and place in style object

Parameters:

• style_obj – style object which will hold data taken from GocadImporter object
• local_prop_idx_list – optional, if set, then will place multiple local property data values in object
• prop_idx – optional, if set, then will place property data in object

_GocadImporter__make_vertex_dict()

Make a dictionary to associate vertex insertion order with vertex sequence number Ordinarily the vertex sequence number is the same as the insertion order in the vertex array, but some GOCAD files have missing vertices etc. The first element starts at ‘1’

_GocadImporter__set_type(file_ext, first_line_str)

Sets the type of GOCAD file: TSURF, VOXEL, PLINE etc.

Parameters:

• fileExt – the file extension
• firstLineStr – first line in the file

Returns:

returns True if it could determine the type of file Will return False when given the header of a GOCAD group file, since cannot create a vessel object from the group file itself, only from the group members

_atom_arr = None

Array of named tuples ‘ATOM’ used to store atom data

_is_pl = None

True iff it is a GOCAD PLINE file

_is_sg = None

True iff it is a GOCAD SGRID file

_is_ts = None

True iff it is a GOCAD TSURF file

_is_vo = None

True iff it is a GOCAD VOXET file

_is_vs = None

True iff it is a GOCAD VSET file

_is_wl = None

True iff it is a GOCAD WELL file

_seg_arr = None

Array of named tuples ‘SEG’ used to store line segment data

_trgl_arr = None

Array of named tuples ‘TRGL’ used store triangle face data

_vrtx_arr = None

Array of named tuples ‘VRTX’ used to store vertex data

axis_max = None

3 dimensional maximum point of voxet volume

axis_min = None

3 dimensional minimum point of voxet volume

axis_o = None

Volume’s origin (X,Y,Z)

axis_u = None

U-axis volume vector

axis_v = None

V-axis volume vector

axis_w = None

W-axis volume vector

calc_sg_xyz(x_idx, y_idx, z_idx, fp_arr)

SGRID has coordinates in points file

calc_vo_xyz(x_idx, y_idx, z_idx, mult)

Calculate the XYZ coords and their maxs & mins

coord_sys_name = None

Name of the GOCAD coordinate system

ct_file_dict = None

A dictionary of files which contain colour tables key is GOCAD filename, val is CSV file

flags_array_length = None

Size of flags file

flags_bit_length = None

Number of bit in use in flags file

flags_bit_size = None

Size (number of bytes) of each element in flags file

flags_file = None

Name of flags file associated with voxel file

flags_offset = None

Offset within the flags file where data starts

flags_prop = None

PROPS object used for the voxet flags file which has region data in it and for SGRID files

gsm_list = None

List of (ModelGeometries, STYLE, METADATA)

handle_exc(exc)

If stop_on_exc is set or debug is on, print details of exception and stop

Parameters:exc – exception

header_name = None

Contents of the name field in the header

invert_zaxis = None

Set to true if z-axis inversion is turned on in this GOCAD file

local_props = None

OrderedDict of PROPS objects for attached PVRTX and PATOM properties

meta_obj = None

Seed copies of ModelGeometries, STYLE, METADATA for data gathering purposes

np_filename = None

Filename of GOCAD file without path or extension

parse_axis_unit(field)

Processes the AXIS_UNIT keyword :param field: array of field strings

parse_colour(colour_str)

Parse a colour string into RGBA tuple.

Parameters:colour_str – colour can either be spaced RGBA/RGB floats, or ‘#’ + 6 digit hex string Returns:a tuple with 4 floats, (R,G,B,A)

parse_float(fp_str, null_val=None)

Converts a string to float, handles infinite values

Parameters:

• fp_str – string to convert to a float
• null_val – value representing ‘no data’

Returns:

a boolean and a float If could not convert then return (False, None) else if ‘null_val’ is defined return (False, null_val)

parse_int(int_str, null_val=None)

Converts a string to an int

Parameters:

• int_str – string to convert to int
• null_val – value representing ‘no data’

Returns:

a boolean and an integer If could not convert then return (False, None) else if ‘null_val’ is defined return (False, null_val)

parse_property_header(prop_obj, line_str)

Parses the PROPERTY header, extracting the colour table info

and storing it in PROPS object

Params prop_obj:  a PROPS object to store the data Params line_str:  current line

parse_props(field, coord_tup, is_patom=False)

This parses a line of properties associated with a PVTRX or PATOM line

Parameters:

• field – array of strings representing line with properties
• coord_tup – (X,Y,Z) float tuple of the coordinates
• is_patom – optional, True if this is from a PATOM, default False

parse_xyz(is_float, x_str, y_str, z_str, do_minmax=False, convert=True)

Helpful function to read XYZ cooordinates

Parameters:

• is_float – if true parse x y z as floats else try integers
• y_str, z_str (x_str,) – X,Y,Z coordinates in string form
• do_minmax – calculate min/max of the X,Y,Z coords
• convert – convert from kms to metres if necessary

Returns:

returns tuple of four parameters: success - true if could convert the strings to floats/ints x,y,z - floating point values, converted to metres if units are kms

points_file = None

Points file (SGRID)

points_offset = None

Offset within points file (SGRID)

process_ascii_well_path(line_gen, field)

Process ascii well path header

Parameters:

• line_gen – line generator
• field – array of field strings from first line of prop class header

Returns:

a boolean, is True iff we are at last line; well_path, list of coordinates of well path; marker_list, list of markers

process_coord_hdr(line_gen)

Process fields within coordinate header.

Parameters:line_gen – line generator Returns:two booleans, the first is True iff reached end of sequence, the second is True iff there is an unrecoverable error

process_gocad(src_dir, filename_str, file_lines)

Extracts details from gocad file. This should be called before other functions!

Parameters:

• filename_str – filename of gocad file
• file_lines – array of strings of lines from gocad file

Returns:

true if could process file, and a list of (geometry, style, metadata) objects

process_header(line_gen)

Process fields in the GOCAD header

Parameters:line_gen – line generator Returns:a boolean, is True iff we are at last line

process_prop_class_hdr(line_gen, field)

Process the property class header

Parameters:

• line_gen – line generator
• field – array of field strings from first line of prop class header

Returns:

a boolean, is True iff we are at last line

process_vol_data(line_gen, field, field_raw, src_dir)

Process all the voxet and sgrid data fields

Parameters:

• line_gen – line generator
• field – array of field strings
• field – array of field strings, not space separated
• src_dir – source directory of voxet file

process_well_binary_file(file_name)

process_well_curve(line_gen, field)

Process well curve

Parameters:

• line_gen – line generator
• field – array of field strings from first line of prop class header

Returns:

a boolean, is True iff we are at last line

process_well_info(field, line_gen)

Process the information after a well marker or well zone is defined

Parameters:

• line_gen – line generator
• field – array of field strings from first line of prop class header

Returns:

a boolean, is True iff we are at last line and info dict

prop_dict = None

Dictionary of PROPS objects, stores GOCAD “PROPERTY” objects from VOXET files Dictionary index is the PROPERTY number e.g. ‘1’, ‘2’, ‘3’ …

read_region_flags_file(flags_array_len, flags_file, flags_bit_sz, flags_offset)

Reads the flags file and looks for regions for a VOXET or SGRID file.

Parameters:

• flags_array_len – length of flags array
• flags_file – filename of flags file
• flags_bit_sz – mumber of bits in each element of flags array
• flags_offset – pointer to start of flags data within flags file

read_volume_binary_files()

Open up and read binary volume file, could be from VOXET or SGRID

Returns:False upon error

region_colour_dict = None

Region colour dict, key is region name, value is RGB (float, float, float)

region_dict = None

Labels and bit numbers for each region in a flags file, key is number (as string), value is label

rock_label_idx = None

Some voxet files have floats that are indexes to rock types

sgrid_cell_align = None

Is SGRID aligned to cells or points ?

stop_on_exc = True

Stop upon exception, regardless of debug level

uses_default_coords = None

Uses default coordinates

vol_sz = None

Size of voxet volume

xyz_mult = None

Used to convert to metres if the units are in kilometres

xyz_unit = None

Units of XYZ axes

imports.gocad.gocad_importer.extract_from_grp(src_dir, filename_str, file_lines, base_xyz, debug_lvl, nondef_coords, ct_file_dict)

Extracts GOCAD files from a GOCAD group file

Parameters:

• src_dir – source directory for GOCAD file
• filename_str – filename of GOCAD file
• file_lines – lines extracted from GOCAD group file
• base_xyz – base coordinates as (x,y,z) tuple added to all 3d coordinates
• debug_lvl – debug level for debug output e.g. logging.DEBUG
• nondefault_coords – optional flag, supports non-default coordinates, default is False
• ct_file_dict – a dictionary of files which contain a tuple: (filename of CSV colour table, list of values to be rendered transparent) key is GOCAD filename

Returns:

a list of (ModelGeometries, STYLE, METADATA) objects

imports.gocad.gocad_importer.is_group_header(line_str)

Returns true iff line string is a GOCAD group header :param line_str: line string :returns: true iif line string is a GOCAD group header

imports.gocad.helpers module

A collection GOCAD helper functions

imports.gocad.helpers.check_vertex(num, vrtx_arr)

If vertex exists in vertex array then returns True else False

Parameters:

• num – vertex number to search for
• vrtx_arr – vertex array

imports.gocad.helpers.make_line_gen(file_lines)

This is a Python generator function that processes lines of the GOCAD object file

and returns each line in various forms, from quite unprocessed to fully processed

Parameters:

• filename_str – filename of gocad file
• file_lines – array of strings of lines from gocad file

Returns:

array of field strings in upper case with double quotes removed from strings, array of field string in original case without double quotes removed, line of GOCAD file in upper case, boolean, True iff it is the last line of the file

imports.gocad.helpers.split_gocad_objs(filename_lines)

Separates joined GOCAD entries within a file

Parameters:filename_lines – lines from concatenated GOCAD file

imports.gocad.parsers module

Functions that process fields in a single line of a GOCAD file

imports.gocad.parsers.parse_axis_unit(self, field)

Processes the AXIS_UNIT keyword :param field: array of field strings

imports.gocad.parsers.parse_colour(self, colour_str)

Parse a colour string into RGBA tuple.

Parameters:colour_str – colour can either be spaced RGBA/RGB floats, or ‘#’ + 6 digit hex string Returns:a tuple with 4 floats, (R,G,B,A)

imports.gocad.parsers.parse_float(self, fp_str, null_val=None)

Converts a string to float, handles infinite values

Parameters:

• fp_str – string to convert to a float
• null_val – value representing ‘no data’

Returns:

a boolean and a float If could not convert then return (False, None) else if ‘null_val’ is defined return (False, null_val)

imports.gocad.parsers.parse_int(self, int_str, null_val=None)

Converts a string to an int

Parameters:

• int_str – string to convert to int
• null_val – value representing ‘no data’

Returns:

a boolean and an integer If could not convert then return (False, None) else if ‘null_val’ is defined return (False, null_val)

imports.gocad.parsers.parse_property_header(self, prop_obj, line_str)

Parses the PROPERTY header, extracting the colour table info

and storing it in PROPS object

Params prop_obj:  a PROPS object to store the data Params line_str:  current line

imports.gocad.parsers.parse_props(self, field, coord_tup, is_patom=False)

This parses a line of properties associated with a PVTRX or PATOM line

Parameters:

• field – array of strings representing line with properties
• coord_tup – (X,Y,Z) float tuple of the coordinates
• is_patom – optional, True if this is from a PATOM, default False

imports.gocad.parsers.parse_xyz(self, is_float, x_str, y_str, z_str, do_minmax=False, convert=True)

Helpful function to read XYZ cooordinates

Parameters:

• is_float – if true parse x y z as floats else try integers
• y_str, z_str (x_str,) – X,Y,Z coordinates in string form
• do_minmax – calculate min/max of the X,Y,Z coords
• convert – convert from kms to metres if necessary

Returns:

returns tuple of four parameters: success - true if could convert the strings to floats/ints x,y,z - floating point values, converted to metres if units are kms

imports.gocad.processors module

Functions to process multiple lines used for specialist purposes

imports.gocad.processors.process_ascii_well_path(self, line_gen, field)

Process ascii well path header

Parameters:

• line_gen – line generator
• field – array of field strings from first line of prop class header

Returns:

a boolean, is True iff we are at last line; well_path, list of coordinates of well path; marker_list, list of markers

imports.gocad.processors.process_coord_hdr(self, line_gen)

Process fields within coordinate header.

Parameters:line_gen – line generator Returns:two booleans, the first is True iff reached end of sequence, the second is True iff there is an unrecoverable error

imports.gocad.processors.process_header(self, line_gen)

Process fields in the GOCAD header

Parameters:line_gen – line generator Returns:a boolean, is True iff we are at last line

imports.gocad.processors.process_prop_class_hdr(self, line_gen, field)

Process the property class header

Parameters:

• line_gen – line generator
• field – array of field strings from first line of prop class header

Returns:

a boolean, is True iff we are at last line

imports.gocad.processors.process_vol_data(self, line_gen, field, field_raw, src_dir)

Process all the voxet and sgrid data fields

Parameters:

• line_gen – line generator
• field – array of field strings
• field – array of field strings, not space separated
• src_dir – source directory of voxet file

imports.gocad.processors.process_well_binary_file(self, file_name)

imports.gocad.processors.process_well_curve(self, line_gen, field)

Process well curve

Parameters:

• line_gen – line generator
• field – array of field strings from first line of prop class header

Returns:

a boolean, is True iff we are at last line

imports.gocad.processors.process_well_info(self, field, line_gen)

Process the information after a well marker or well zone is defined

Parameters:

• line_gen – line generator
• field – array of field strings from first line of prop class header

Returns:

a boolean, is True iff we are at last line and info dict

imports.gocad.processors.to_dia(sdia)

Converts a 4-tuple to 3-tuple of floats

Parameters:sdia – 4-tuple (‘STATION’, d, i, a) Returns:True/False, three float tuple

imports.gocad.processors.to_xyz_min_curve(dia1, dia2)

Convert measured depth, inclination, azimuth to x,y,z via minimum curvature method

Parameters:

• dia1 – tuple (measured depth, inclination, azimuth) measured depth, metres, float inclination, degrees, float, 0 = vertical, 90 = horizontal azimuth, degrees, float, measured from North
• dia2 – tuple (measured depth, inclination, azimuth)

imports.gocad.props module

Contains the PROPS class

class imports.gocad.props.PROPS(class_name, debug_level)

Bases: object

This class holds generic 3d data and properties e.g. information extracted from 3d binary files (e.g. from GOCAD ‘PROP_FILE’) information attached to a set of XYZ points (e.g. from GOCAD ‘PATOM’, ‘PVRTX’)

_PROPS__calc_minmax(fltp)

Calculates minimum & maximum of floating point value and stores result locally in ‘data_stats’ fp - floating point value (numpy or python float)

append_to_ijk(ijk, val)

Appends a value to xyz dict ijk - (I,J,K) tuple array indexes (ints) val - value to be assigned

append_to_xyz(xyz, val)

Appends a value to xyz dict xyz - (X,Y,Z) tuple array indexes (floats) val - value to be assigned

assign_to_3d(x_val, y_val, z_val, fltp)

Assigns a value to 3d array x,y,z - XYZ integer array indexes fltp - floating point value to be assigned

assign_to_ijk(ijk, val)

Assigns a value to ijk dict ijk - (I,J,K) tuple array indexes (ints) val - value to be assigned (float or tuple)

assign_to_xyz(xyz, val)

Assigns a value to xyz dict xyz - (X,Y,Z) tuple array indexes (floats) val - value to be assigned (float or tuple)

class_name = None

Property class names

colour_map = None

If colour map was specified, then it is stored here, integer is the key, value is (R,G,B,A) where R, G, B, A are floats

colourmap_name = None

Name of colour map

data_3d = None

Property data collected from binary file, value is float, stored as a 3d numpy array.

data_ijk = None

Property data attached to XYZ points (index is IJK int indexes)

data_stats = None

Property data statistics: min & max

data_sz = None

Number of bytes in number in binary file, usually 1, 2 or 4

data_type = None

Type of data in binary file e.g. ‘h’ = short 2-byte int, ‘f’ = float, ‘b’ - byte, ‘rgba’ - 4-byte RGBA

data_xyz = None

Property data attached to XYZ points (index is XYZ coordinate)

file_name = None

Name of binary file associated with GOCAD file

get_str_data_type()

Returns a string form of the data type of the volume data e.g. “INT_16”, “FLOAT_32”, “UINT_8”, “RGBA”

is_index_data = None

Uses ‘data_3d’ to hold index to colour table or rock label table

make_numpy_dtype()

Returns a string that can be passed to ‘numpy’ to read a binary file It takes the ‘data_type’ of ‘f’, ‘b’, h’ & ‘rgba’

no_data_marker = None

Value representing ‘no data’ values

offset = None

Offset within binary file

read_colour_table_csv(csv_file, transp_list)

Reads an RGB colour table from CSV file for use in VOXET colours CSV Format: col#1: integer index, col#2: R-value, col#3: G-value, col#4: B-value csv_file - filename of CSV file to read, without path Sets the ‘colour_map’ and ‘rock_label_table’ class attibutes ‘colour_map’ is a dict, key is integer, value is (R,G,B,A) tuple of floats ‘rock_label_table’ is a dict, key is integer, value is string

rock_label_table = None

Table specifying names of rocks , key is an integer, value is the label

signed_int = None

Is True iff binary data is a signed integer else False

imports.gocad.volumes module

imports.gocad.volumes.calc_sg_xyz(self, x_idx, y_idx, z_idx, fp_arr)

SGRID has coordinates in points file

imports.gocad.volumes.calc_vo_xyz(self, x_idx, y_idx, z_idx, mult)

Calculate the XYZ coords and their maxs & mins

imports.gocad.volumes.read_region_flags_file(self, flags_array_len, flags_file, flags_bit_sz, flags_offset)

Reads the flags file and looks for regions for a VOXET or SGRID file.

Parameters:

• flags_array_len – length of flags array
• flags_file – filename of flags file
• flags_bit_sz – mumber of bits in each element of flags array
• flags_offset – pointer to start of flags data within flags file

imports.gocad.volumes.read_volume_binary_files(self)

Open up and read binary volume file, could be from VOXET or SGRID

Returns:False upon error

Module contents