From f37413b2aa03c24de6c9ea1e94053d7607b4d9b2 Mon Sep 17 00:00:00 2001 From: Dongdong Tian Date: Sun, 15 Oct 2023 19:14:33 +0800 Subject: [PATCH] Change ncols to names --- pygmt/clib/session.py | 9 +++--- pygmt/helpers/utils.py | 64 +++++++++++++++++++++++++-------------- pygmt/src/blockm.py | 2 +- pygmt/src/contour.py | 2 +- pygmt/src/nearneighbor.py | 2 +- pygmt/src/plot.py | 12 ++++---- pygmt/src/plot3d.py | 12 ++++---- pygmt/src/project.py | 2 +- pygmt/src/rose.py | 5 ++- pygmt/src/sphdistance.py | 2 +- pygmt/src/surface.py | 2 +- pygmt/src/text.py | 8 ++--- pygmt/src/triangulate.py | 2 +- pygmt/src/wiggle.py | 2 +- pygmt/src/xyz2grd.py | 2 +- 15 files changed, 75 insertions(+), 53 deletions(-) diff --git a/pygmt/clib/session.py b/pygmt/clib/session.py index 0988d87728d..c2a0ba12427 100644 --- a/pygmt/clib/session.py +++ b/pygmt/clib/session.py @@ -1476,7 +1476,7 @@ def virtualfile_from_data( check_kind=None, data=None, vectors=None, - ncols=2, + names=["x", "y"], required_data=True, ): """ @@ -1498,8 +1498,9 @@ def virtualfile_from_data( vectors : list of 1-D arrays or None A list of 1-D arrays. Each array will be a column in the table. All of these arrays must be of the same size. - ncols : int - The minimum number of columns required for the data. + names : list of str + A list of names for each of the columns. Must be of the same size + as the number of vectors. Default is ``["x", "y"]``. required_data : bool Set to True when 'data' is required, or False when dealing with optional virtual files. [Default is True]. @@ -1537,7 +1538,7 @@ def virtualfile_from_data( validate_data_input( data=data, vectors=vectors, - ncols=ncols, + names=names, required_data=required_data, kind=kind, ) diff --git a/pygmt/helpers/utils.py b/pygmt/helpers/utils.py index d6b7ab8ce5a..6926f1a1911 100644 --- a/pygmt/helpers/utils.py +++ b/pygmt/helpers/utils.py @@ -16,30 +16,49 @@ def validate_data_input( - data=None, vectors=None, ncols=2, required_data=True, kind=None + data=None, vectors=None, names=["x", "y"], required_data=True, kind=None ): """ Check if the data input is valid. + Parameters + ---------- + data : str, pathlib.PurePath, None, bool, xarray.DataArray or {table-like} + Pass in either a file name or :class:`pathlib.Path` to an ASCII data + table, an :class:`xarray.DataArray`, a 1-D/2-D + {table-classes} or an option argument. + vectors : list of 1-D arrays + A list of 1-D arrays with the data columns. + names : list of str + List of column names. + required_data : bool + Set to True when 'data' is required, or False when dealing with + optional virtual files. [Default is True]. + kind : str or None + The kind of data that will be passed to a module. If not given, it + will be determined by calling :func:`data_kind`. + Examples -------- >>> validate_data_input(data="infile") - >>> validate_data_input(vectors=[[1, 2, 3], [4, 5, 6]], ncols=2) - >>> validate_data_input(vectors=[[1, 2, 3], [4, 5, 6], [7, 8, 9]], ncols=3) + >>> validate_data_input(vectors=[[1, 2, 3], [4, 5, 6]], names="xy") + >>> validate_data_input( + ... vectors=[[1, 2, 3], [4, 5, 6], [7, 8, 9]], names="xyz" + ... ) >>> validate_data_input(data=None, required_data=False) >>> validate_data_input() Traceback (most recent call last): ... pygmt.exceptions.GMTInvalidInput: No input data provided. - >>> validate_data_input(vectors=[[1, 2, 3], None], ncols=2) + >>> validate_data_input(vectors=[[1, 2, 3], None], names="xy") Traceback (most recent call last): ... pygmt.exceptions.GMTInvalidInput: The 'y' column can't be None. - >>> validate_data_input(vectors=[None, [4, 5, 6]], ncols=2) + >>> validate_data_input(vectors=[None, [4, 5, 6]], names="xy") Traceback (most recent call last): ... pygmt.exceptions.GMTInvalidInput: The 'x' column can't be None. - >>> validate_data_input(vectors=[[1, 2, 3], [4, 5, 6], None], ncols=3) + >>> validate_data_input(vectors=[[1, 2, 3], [4, 5, 6], None], names="xyz") Traceback (most recent call last): ... pygmt.exceptions.GMTInvalidInput: The 'z' column can't be None. @@ -47,13 +66,13 @@ def validate_data_input( >>> import pandas as pd >>> import xarray as xr >>> data = np.arange(8).reshape((4, 2)) - >>> validate_data_input(data=data, ncols=3, kind="matrix") + >>> validate_data_input(data=data, names="xyz", kind="matrix") Traceback (most recent call last): ... pygmt.exceptions.GMTInvalidInput: data must have at least 3 columns. >>> validate_data_input( ... data=pd.DataFrame(data, columns=["x", "y"]), - ... ncols=3, + ... names="xyz", ... kind="matrix", ... ) Traceback (most recent call last): @@ -61,7 +80,7 @@ def validate_data_input( pygmt.exceptions.GMTInvalidInput: data must have at least 3 columns. >>> validate_data_input( ... data=xr.Dataset(pd.DataFrame(data, columns=["x", "y"])), - ... ncols=3, + ... names="xyz", ... kind="matrix", ... ) Traceback (most recent call last): @@ -91,28 +110,27 @@ def validate_data_input( if kind == "vectors": # From data_kind, we know that data is None if vectors is None: raise GMTInvalidInput("No input data provided.") - if len(vectors) < ncols: + if len(vectors) < len(names): raise GMTInvalidInput( - f"Requires {ncols} 1-D arrays but got {len(vectors)}." + f"Requires {len(names)} 1-D arrays but got {len(vectors)}." ) - for i, v in enumerate(vectors[:ncols]): + for i, v in enumerate(vectors[: len(names)]): if v is None: - if i < 3: - msg = f"The '{'xyz'[i]}' column can't be None." - else: - msg = "Column {i} can't be None." - raise GMTInvalidInput(msg) + raise GMTInvalidInput(f"Column {i} ('{names[i]}') can't be None.") else: if vectors is not None and any(v is not None for v in vectors): raise GMTInvalidInput("Too much data. Pass in either 'data' or 1-D arrays.") if kind == "matrix": # check number of columns for matrix-like data + msg = f"data must have at least {len(names)} columns.\n" + " ".join(names) if hasattr(data, "shape"): # np.ndarray or pd.DataFrame - if len(data.shape) == 1 and data.shape[0] < ncols: - raise GMTInvalidInput(f"data must have at least {ncols} columns.") - if len(data.shape) > 1 and data.shape[1] < ncols: - raise GMTInvalidInput(f"data must have at least {ncols} columns.") - if hasattr(data, "data_vars") and len(data.data_vars) < ncols: # xr.Dataset - raise GMTInvalidInput(f"data must have at least {ncols} columns.") + if len(data.shape) == 1 and data.shape[0] < len(names): + raise GMTInvalidInput(msg) + if len(data.shape) > 1 and data.shape[1] < len(names): + raise GMTInvalidInput(msg) + if hasattr(data, "data_vars") and len(data.data_vars) < len( + names + ): # xr.Dataset + raise GMTInvalidInput(msg) def data_kind(data=None, required=True): diff --git a/pygmt/src/blockm.py b/pygmt/src/blockm.py index d8462445ed6..bfe1be138dd 100644 --- a/pygmt/src/blockm.py +++ b/pygmt/src/blockm.py @@ -44,7 +44,7 @@ def _blockm(block_method, data, x, y, z, outfile, **kwargs): with GMTTempFile(suffix=".csv") as tmpfile: with Session() as lib: table_context = lib.virtualfile_from_data( - check_kind="vector", data=data, vectors=[x, y, z], ncols=3 + check_kind="vector", data=data, vectors=[x, y, z], names="xyz" ) # Run blockm* on data table with table_context as infile: diff --git a/pygmt/src/contour.py b/pygmt/src/contour.py index ac34dcb5d95..3e88c45aec5 100644 --- a/pygmt/src/contour.py +++ b/pygmt/src/contour.py @@ -116,7 +116,7 @@ def contour(self, data=None, x=None, y=None, z=None, **kwargs): with Session() as lib: file_context = lib.virtualfile_from_data( - check_kind="vector", data=data, vectors=[x, y, z], ncols=3 + check_kind="vector", data=data, vectors=[x, y, z], names="xyz" ) with file_context as fname: lib.call_module( diff --git a/pygmt/src/nearneighbor.py b/pygmt/src/nearneighbor.py index b53b8ec4a9f..d266cce075c 100644 --- a/pygmt/src/nearneighbor.py +++ b/pygmt/src/nearneighbor.py @@ -150,7 +150,7 @@ def nearneighbor(data=None, x=None, y=None, z=None, **kwargs): with GMTTempFile(suffix=".nc") as tmpfile: with Session() as lib: table_context = lib.virtualfile_from_data( - check_kind="vector", data=data, vectors=[x, y, z], ncols=3 + check_kind="vector", data=data, vectors=[x, y, z], names="xyz" ) with table_context as infile: if (outgrid := kwargs.get("G")) is None: diff --git a/pygmt/src/plot.py b/pygmt/src/plot.py index 3e998122486..5c7bfb20351 100644 --- a/pygmt/src/plot.py +++ b/pygmt/src/plot.py @@ -215,11 +215,11 @@ def plot(self, data=None, x=None, y=None, size=None, direction=None, **kwargs): kind = data_kind(data) vectors = [x, y] - ncols = 2 + names = ["x", "y"] if kwargs.get("S") is not None and kwargs["S"][0] in "vV" and direction is not None: vectors.extend(direction) - ncols += 2 + names.extend(["x2", "y2"]) elif ( kwargs.get("S") is None and kind == "geojson" @@ -242,7 +242,7 @@ def plot(self, data=None, x=None, y=None, size=None, direction=None, **kwargs): "Can't use arrays for fill if data is matrix or file." ) vectors.append(kwargs["G"]) - ncols += 1 + names.append("fill") del kwargs["G"] if size is not None: if kind != "vectors": @@ -250,7 +250,7 @@ def plot(self, data=None, x=None, y=None, size=None, direction=None, **kwargs): "Can't use arrays for 'size' if data is a matrix or file." ) vectors.append(size) - ncols += 1 + names.append("size") for flag in ["I", "t"]: if kwargs.get(flag) is not None and is_nonstr_iter(kwargs[flag]): @@ -259,12 +259,12 @@ def plot(self, data=None, x=None, y=None, size=None, direction=None, **kwargs): f"Can't use arrays for {plot.aliases[flag]} if data is matrix or file." ) vectors.append(kwargs[flag]) - ncols += 1 + names.append(plot.aliases[flag]) kwargs[flag] = "" with Session() as lib: file_context = lib.virtualfile_from_data( - check_kind="vector", data=data, vectors=vectors, ncols=ncols + check_kind="vector", data=data, vectors=vectors, names=names ) with file_context as fname: diff --git a/pygmt/src/plot3d.py b/pygmt/src/plot3d.py index 215b659ac8f..1cbce57bc6e 100644 --- a/pygmt/src/plot3d.py +++ b/pygmt/src/plot3d.py @@ -185,11 +185,11 @@ def plot3d( kind = data_kind(data) vectors = [x, y, z] - ncols = 3 + names = ["x", "y", "z"] if kwargs.get("S") is not None and kwargs["S"][0] in "vV" and direction is not None: vectors.extend(direction) - ncols += 2 + names.extend(["x2", "y2"]) elif ( kwargs.get("S") is None and kind == "geojson" @@ -212,15 +212,15 @@ def plot3d( "Can't use arrays for fill if data is matrix or file." ) vectors.append(kwargs["G"]) - ncols += 1 + names.append("fill") del kwargs["G"] if size is not None: if kind != "vectors": raise GMTInvalidInput( "Can't use arrays for 'size' if data is a matrix or a file." ) - ncols += 1 vectors.append(size) + names.append("size") for flag in ["I", "t"]: if kwargs.get(flag) is not None and is_nonstr_iter(kwargs[flag]): @@ -229,12 +229,12 @@ def plot3d( f"Can't use arrays for {plot3d.aliases[flag]} if data is matrix or file." ) vectors.append(kwargs[flag]) - ncols += 1 + names.append(plot3d.aliases[flag]) kwargs[flag] = "" with Session() as lib: file_context = lib.virtualfile_from_data( - check_kind="vector", data=data, vectors=vectors, ncols=ncols + check_kind="vector", data=data, vectors=vectors, names=names ) with file_context as fname: diff --git a/pygmt/src/project.py b/pygmt/src/project.py index dd7f665fd4b..c5ecd8cb83a 100644 --- a/pygmt/src/project.py +++ b/pygmt/src/project.py @@ -228,7 +228,7 @@ def project(data=None, x=None, y=None, z=None, outfile=None, **kwargs): with Session() as lib: if kwargs.get("G") is None: table_context = lib.virtualfile_from_data( - check_kind="vector", data=data, vectors=[x, y, z], ncols=3 + check_kind="vector", data=data, vectors=[x, y, z], names="xyz" ) # Run project on the temporary (csv) data table diff --git a/pygmt/src/rose.py b/pygmt/src/rose.py index 4a9b39d2cfd..01862152543 100644 --- a/pygmt/src/rose.py +++ b/pygmt/src/rose.py @@ -203,7 +203,10 @@ def rose(self, data=None, length=None, azimuth=None, **kwargs): with Session() as lib: file_context = lib.virtualfile_from_data( - check_kind="vector", data=data, vectors=[length, azimuth], ncols=2 + check_kind="vector", + data=data, + vectors=[length, azimuth], + names=["length", "azimuth"], ) with file_context as fname: diff --git a/pygmt/src/sphdistance.py b/pygmt/src/sphdistance.py index 46f2ee2abc2..a7179496531 100644 --- a/pygmt/src/sphdistance.py +++ b/pygmt/src/sphdistance.py @@ -120,7 +120,7 @@ def sphdistance(data=None, x=None, y=None, **kwargs): with GMTTempFile(suffix=".nc") as tmpfile: with Session() as lib: file_context = lib.virtualfile_from_data( - check_kind="vector", data=data, vectors=[x, y], ncols=2 + check_kind="vector", data=data, vectors=[x, y], names="xy" ) with file_context as infile: if (outgrid := kwargs.get("G")) is None: diff --git a/pygmt/src/surface.py b/pygmt/src/surface.py index 32b099c2af0..62341a52b95 100644 --- a/pygmt/src/surface.py +++ b/pygmt/src/surface.py @@ -165,7 +165,7 @@ def surface(data=None, x=None, y=None, z=None, **kwargs): with GMTTempFile(suffix=".nc") as tmpfile: with Session() as lib: file_context = lib.virtualfile_from_data( - check_kind="vector", data=data, vectors=[x, y, z], ncols=3 + check_kind="vector", data=data, vectors=[x, y, z], names="xyz" ) with file_context as infile: if (outgrid := kwargs.get("G")) is None: diff --git a/pygmt/src/text.py b/pygmt/src/text.py index f4a368aa16f..21e652bb8e4 100644 --- a/pygmt/src/text.py +++ b/pygmt/src/text.py @@ -222,24 +222,24 @@ def text_( kwargs["F"] += f"+c{position}+t{text}" vectors = [x, y] - ncols = 2 + names = ["x", "y"] # If an array of transparency is given, GMT will read it from # the last numerical column per data record. if kwargs.get("t") is not None and is_nonstr_iter(kwargs["t"]): vectors.append(kwargs["t"]) kwargs["t"] = "" - ncols += 1 + names.append("transparency") # Append text at last column. Text must be passed in as str type. if kind == "vectors": vectors.append( np.vectorize(non_ascii_to_octal)(np.atleast_1d(text).astype(str)) ) - ncols += 1 + names.append("text") with Session() as lib: file_context = lib.virtualfile_from_data( - check_kind="vector", data=textfiles, vectors=vectors, ncols=ncols + check_kind="vector", data=textfiles, vectors=vectors, names=names ) with file_context as fname: lib.call_module(module="text", args=build_arg_string(kwargs, infile=fname)) diff --git a/pygmt/src/triangulate.py b/pygmt/src/triangulate.py index 3f47926e90b..da980730638 100644 --- a/pygmt/src/triangulate.py +++ b/pygmt/src/triangulate.py @@ -127,7 +127,7 @@ def _triangulate( """ with Session() as lib: table_context = lib.virtualfile_from_data( - check_kind="vector", data=data, vectors=[x, y, z], ncols=3 + check_kind="vector", data=data, vectors=[x, y, z], names="xyz" ) with table_context as infile: # table output if outgrid is unset, else output to outgrid diff --git a/pygmt/src/wiggle.py b/pygmt/src/wiggle.py index 2b2577a0b2c..74cd5c34223 100644 --- a/pygmt/src/wiggle.py +++ b/pygmt/src/wiggle.py @@ -122,7 +122,7 @@ def wiggle( with Session() as lib: file_context = lib.virtualfile_from_data( - check_kind="vector", data=data, vectors=[x, y, z], ncols=3 + check_kind="vector", data=data, vectors=[x, y, z], names="xyz" ) with file_context as fname: diff --git a/pygmt/src/xyz2grd.py b/pygmt/src/xyz2grd.py index b0cf1f51ff2..e0b0d041353 100644 --- a/pygmt/src/xyz2grd.py +++ b/pygmt/src/xyz2grd.py @@ -154,7 +154,7 @@ def xyz2grd(data=None, x=None, y=None, z=None, **kwargs): with GMTTempFile(suffix=".nc") as tmpfile: with Session() as lib: file_context = lib.virtualfile_from_data( - check_kind="vector", data=data, vectors=[x, y, z], ncols=3 + check_kind="vector", data=data, vectors=[x, y, z], names="xyz" ) with file_context as infile: if (outgrid := kwargs.get("G")) is None: