JuliaAstro / FITSIO.jl / 166

Committed 26 Jul 2017 - 19:32 coverage: 72.418%. Remained the same

Build # 166

Build Type

Pull #77

travis-ci

Committed by

web-flow

Commit Message

Minor change

Pull Request Pull Request #77: [WIP] Add Documenter to build documentation

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73.75

/src/image.jl

# ImageHDU methods

# Display the image datatype and dimensions
function show(io::IO, hdu::ImageHDU)
    fits_assert_open(hdu.fitsfile)
    fits_movabs_hdu(hdu.fitsfile, hdu.ext)
    bitpix = fits_get_img_type(hdu.fitsfile)
    equivbitpix = fits_get_img_equivtype(hdu.fitsfile)
    sz = fits_get_img_size(hdu.fitsfile)

    if bitpix == equivbitpix
        datainfo = string(TYPE_FROM_BITPIX[equivbitpix])
    else
        datainfo = @sprintf("%s (physical: %s)",
                            TYPE_FROM_BITPIX[equivbitpix],
                            TYPE_FROM_BITPIX[bitpix])
    end

    print(io, """
    File: $(fits_file_name(hdu.fitsfile))
    HDU: $(hdu.ext)$(fits_get_ext_info_string(hdu.fitsfile))
    Type: Image
    Datatype: $datainfo
    Datasize: $(tuple(sz...))
    """)
end

# Get image dimensions
function ndims(hdu::ImageHDU)
    fits_assert_open(hdu.fitsfile)
    fits_movabs_hdu(hdu.fitsfile, hdu.ext)
    fits_get_img_dim(hdu.fitsfile)
end

# Get image size
function size(hdu::ImageHDU)
    fits_assert_open(hdu.fitsfile)
    fits_movabs_hdu(hdu.fitsfile, hdu.ext)
    sz = fits_get_img_size(hdu.fitsfile)
    tuple(sz...)
end

function size(hdu::ImageHDU, i::Integer)
    fits_assert_open(hdu.fitsfile)
    fits_movabs_hdu(hdu.fitsfile, hdu.ext)
    sz = fits_get_img_size(hdu.fitsfile)
    sz[i]
end

# `endof` is needed so that hdu[:] can throw DimensionMismatch
# when ndim != 1, rather than no method.
length(hdu::ImageHDU) = prod(size(hdu))
endof(hdu::ImageHDU) = length(hdu::ImageHDU)

# Read a full image from an HDU
function read(hdu::ImageHDU)
    fits_assert_open(hdu.fitsfile)
    fits_movabs_hdu(hdu.fitsfile, hdu.ext)
    sz = fits_get_img_size(hdu.fitsfile)
    bitpix = fits_get_img_equivtype(hdu.fitsfile)
    data = Array{TYPE_FROM_BITPIX[bitpix]}(sz...)
    fits_read_pix(hdu.fitsfile, data)
    data
end

# _checkbounds methods copied from Julia v0.4 Base.
_checkbounds(sz, i::Integer) = 1 <= i <= sz
_checkbounds(sz, i::Colon) = true
_checkbounds(sz, r::Range{Int}) =
    (isempty(r) || (minimum(r) >= 1 && maximum(r) <= sz))

# helper functions for constructing cfitsio indexing vectors in read(hdu, ...)
_first(i::Union{Integer, Range}) = first(i)
_first(::Colon) = 1
_last(sz, i::Union{Integer, Range}) = last(i)
_last(sz, ::Colon) = sz
_step(r::Range) = step(r)
_step(::Union{Integer, Colon}) = 1

# Shape of array to create for read(hdu, ...), dropping trailing
# scalars. This is simpler than in Base because we are guaranteed that
# length(I) == length(sz).
@inline _index_shape(sz, I...) = _index_shape_dim(sz, 1, I...)
_index_shape_dim(sz, dim, I::Integer...) = ()
_index_shape_dim(sz, dim, ::Colon) = (sz[dim],)
_index_shape_dim(sz, dim, r::Range) = (length(r),)
@inline _index_shape_dim(sz, dim, ::Colon, I...) =
    tuple(sz[dim], _index_shape_dim(sz, dim+1, I...)...)
if VERSION >= v"0.5.0-dev"  # In Julia v0.5+ drop scalar-indexed dimensions.
    @inline _index_shape_dim(sz, dim, ::Integer, I...) =
        _index_shape_dim(sz, dim+1, I...)
else
    @inline _index_shape_dim(sz, dim, ::Integer, I...) =
        tuple(1, _index_shape_dim(sz, dim+1, I...)...)
end
@inline _index_shape_dim(sz, dim, r::Range, I...) =
    tuple(length(r), _index_shape_dim(sz, dim+1, I...)...)

# Read a subset of an ImageHDU
function read_internal(hdu::ImageHDU, I::Union{Range{Int}, Integer, Colon}...)
    fits_assert_open(hdu.fitsfile)
    fits_movabs_hdu(hdu.fitsfile, hdu.ext)
    sz = fits_get_img_size(hdu.fitsfile)

    # check number of indices and bounds. Note that number of indices and
    # array dimension must match, unlike in Arrays. Array-like behavior could
    # be supported in the future with care taken in constructing first, last,
    if length(I) != length(sz)
        throw(DimensionMismatch("number of indices must match dimensions"))
    end
    for i=1:length(sz)
        _checkbounds(sz[i], I[i]) || throw(BoundsError())
    end

    # construct first, last and step vectors
    firsts = Clong[_first(idx) for idx in I]
    lasts = Clong[_last(sz[i], I[i]) for i=1:length(sz)]
    steps = Clong[_step(idx) for idx in I]

    # construct output array
    bitpix = fits_get_img_equivtype(hdu.fitsfile)
    data = Array{TYPE_FROM_BITPIX[bitpix]}(_index_shape(sz, I...))

    fits_read_subset(hdu.fitsfile, firsts, lasts, steps, data)
    data
end

# general method and version that returns a single value rather than 0-d array
read(hdu::ImageHDU, I::Union{Range{Int}, Int, Colon}...) =
    read_internal(hdu, I...)
read(hdu::ImageHDU, I::Int...) = read_internal(hdu, I...)[1]

# Add a new ImageHDU to a FITS object
# The following Julia data types are supported for writing images by cfitsio:
# Uint8, Int8, Uint16, Int16, Uint32, Int32, Int64, Float32, Float64
function write{T}(f::FITS, data::Array{T};
                  header::Union{Void, FITSHeader}=nothing,
                  name::Union{Void, String}=nothing,
                  ver::Union{Void, Integer}=nothing)
    fits_assert_open(f.fitsfile)
    s = size(data)
    fits_create_img(f.fitsfile, T, [s...])
    if isa(header, FITSHeader)
        fits_write_header(f.fitsfile, header, true)
    end
    if isa(name, String)
        fits_update_key(f.fitsfile, "EXTNAME", name)
    end
    if isa(ver, Integer)
        fits_update_key(f.fitsfile, "EXTVER", ver)
    end
    fits_write_pix(f.fitsfile, ones(Int, length(s)), length(data), data)
    nothing
end

# Copy a rectangular section of an image and write it to a new FITS
# primary image or image extension. The new image HDU is appended to
# the end of the output file; all the keywords in the input image will
# be copied to the output image. The common WCS keywords will be
# updated if necessary to correspond to the coordinates of the section.

# convert a range to a string that cfitsio understands
cfitsio_range_string(r::UnitRange) = @sprintf "%d:%d" first(r) last(r)
cfitsio_range_string(r::StepRange) =
    @sprintf "%d:%d:%d" first(r) last(r) step(r)

function copy_section(hdu::ImageHDU, dest::FITS, r::Range{Int}...)
    fits_assert_open(hdu.fitsfile)
    fits_assert_open(dest.fitsfile)
    fits_movabs_hdu(hdu.fitsfile, hdu.ext)
    fits_copy_image_section(hdu.fitsfile, dest.fitsfile,
                            join([cfitsio_range_string(ri) for ri in r], ','))
end

1	# ImageHDU methods
2
3	# Display the image datatype and dimensions
4	function show(io::IO, hdu::ImageHDU)
5	fits_assert_open(hdu.fitsfile)	!
6	fits_movabs_hdu(hdu.fitsfile, hdu.ext)	!
7	bitpix = fits_get_img_type(hdu.fitsfile)	!
8	equivbitpix = fits_get_img_equivtype(hdu.fitsfile)	!
9	sz = fits_get_img_size(hdu.fitsfile)	!
10
11	if bitpix == equivbitpix	!
12	datainfo = string(TYPE_FROM_BITPIX[equivbitpix])	!
13	else
14	datainfo = @sprintf("%s (physical: %s)",	!
15	TYPE_FROM_BITPIX[equivbitpix],
16	TYPE_FROM_BITPIX[bitpix])
17	end
18
19	print(io, """	!
20	File: $(fits_file_name(hdu.fitsfile))
21	HDU: $(hdu.ext)$(fits_get_ext_info_string(hdu.fitsfile))
22	Type: Image
23	Datatype: $datainfo
24	Datasize: $(tuple(sz...))
25	""")
26	end
27
28	# Get image dimensions
29	function ndims(hdu::ImageHDU)
30	fits_assert_open(hdu.fitsfile)	!
31	fits_movabs_hdu(hdu.fitsfile, hdu.ext)	!
32	fits_get_img_dim(hdu.fitsfile)	!
33	end
34
35	# Get image size
36	function size(hdu::ImageHDU)
37	fits_assert_open(hdu.fitsfile)	45×
38	fits_movabs_hdu(hdu.fitsfile, hdu.ext)	63×
39	sz = fits_get_img_size(hdu.fitsfile)	63×
40	tuple(sz...)	63×
41	end
42
43	function size(hdu::ImageHDU, i::Integer)
44	fits_assert_open(hdu.fitsfile)	!
45	fits_movabs_hdu(hdu.fitsfile, hdu.ext)	!
46	sz = fits_get_img_size(hdu.fitsfile)	!
47	sz[i]	!
48	end
49
50	# `endof` is needed so that hdu[:] can throw DimensionMismatch
51	# when ndim != 1, rather than no method.
52	length(hdu::ImageHDU) = prod(size(hdu))	!
53	endof(hdu::ImageHDU) = length(hdu::ImageHDU)	!
54
55	# Read a full image from an HDU
56	function read(hdu::ImageHDU)
57	fits_assert_open(hdu.fitsfile)	65×
58	fits_movabs_hdu(hdu.fitsfile, hdu.ext)	91×
59	sz = fits_get_img_size(hdu.fitsfile)	91×
60	bitpix = fits_get_img_equivtype(hdu.fitsfile)	91×
61	data = Array{TYPE_FROM_BITPIX[bitpix]}(sz...)	91×
62	fits_read_pix(hdu.fitsfile, data)	91×
63	data	91×
64	end
65
66	# _checkbounds methods copied from Julia v0.4 Base.
67	_checkbounds(sz, i::Integer) = 1 <= i <= sz	270×
68	_checkbounds(sz, i::Colon) = true	all except 166.1 and 166.4 - 135×
69	_checkbounds(sz, r::Range{Int}) =	180×
70	(isempty(r) \|\| (minimum(r) >= 1 && maximum(r) <= sz))
71
72	# helper functions for constructing cfitsio indexing vectors in read(hdu, ...)
73	_first(i::Union{Integer, Range}) = first(i)	315×
74	_first(::Colon) = 1	all except 166.1 and 166.4 - 135×
75	_last(sz, i::Union{Integer, Range}) = last(i)	315×
76	_last(sz, ::Colon) = sz	225×
77	_step(r::Range) = step(r)	135×
78	_step(::Union{Integer, Colon}) = 1	all except 166.1 and 166.4 - 243×
79
80	# Shape of array to create for read(hdu, ...), dropping trailing
81	# scalars. This is simpler than in Base because we are guaranteed that
82	# length(I) == length(sz).
83	@inline _index_shape(sz, I...) = _index_shape_dim(sz, 1, I...)	270×
84	_index_shape_dim(sz, dim, I::Integer...) = ()	all except 166.1 and 166.4 - 54×
85	_index_shape_dim(sz, dim, ::Colon) = (sz[dim],)	90×
86	_index_shape_dim(sz, dim, r::Range) = (length(r),)	90×
87	@inline _index_shape_dim(sz, dim, ::Colon, I...) =	135×
88	tuple(sz[dim], _index_shape_dim(sz, dim+1, I...)...)
89	if VERSION >= v"0.5.0-dev" # In Julia v0.5+ drop scalar-indexed dimensions.
90	@inline _index_shape_dim(sz, dim, ::Integer, I...) =	45×
91	_index_shape_dim(sz, dim+1, I...)
92	else
93	@inline _index_shape_dim(sz, dim, ::Integer, I...) =	!
94	tuple(1, _index_shape_dim(sz, dim+1, I...)...)
95	end
96	@inline _index_shape_dim(sz, dim, r::Range, I...) =	45×
97	tuple(length(r), _index_shape_dim(sz, dim+1, I...)...)
98
99	# Read a subset of an ImageHDU
100	function read_internal(hdu::ImageHDU, I::Union{Range{Int}, Integer, Colon}...)
101	fits_assert_open(hdu.fitsfile)	450×
102	fits_movabs_hdu(hdu.fitsfile, hdu.ext)	630×
103	sz = fits_get_img_size(hdu.fitsfile)	630×
104
105	# check number of indices and bounds. Note that number of indices and
106	# array dimension must match, unlike in Arrays. Array-like behavior could
107	# be supported in the future with care taken in constructing first, last,
108	if length(I) != length(sz)	630×
109	throw(DimensionMismatch("number of indices must match dimensions"))	126×
110	end
111	for i=1:length(sz)	1,980×
112	_checkbounds(sz[i], I[i]) \|\| throw(BoundsError())	3,177×
113	end
114
115	# construct first, last and step vectors
116	firsts = Clong[_first(idx) for idx in I]	378×
117	lasts = Clong[_last(sz[i], I[i]) for i=1:length(sz)]	6,264×
118	steps = Clong[_step(idx) for idx in I]	378×
119
120	# construct output array
121	bitpix = fits_get_img_equivtype(hdu.fitsfile)	378×
122	data = Array{TYPE_FROM_BITPIX[bitpix]}(_index_shape(sz, I...))	378×
123
124	fits_read_subset(hdu.fitsfile, firsts, lasts, steps, data)	378×
125	data	378×
126	end
127
128	# general method and version that returns a single value rather than 0-d array
129	read(hdu::ImageHDU, I::Union{Range{Int}, Int, Colon}...) =	360×
130	read_internal(hdu, I...)
131	read(hdu::ImageHDU, I::Int...) = read_internal(hdu, I...)[1]	90×
132
133	# Add a new ImageHDU to a FITS object
134	# The following Julia data types are supported for writing images by cfitsio:
135	# Uint8, Int8, Uint16, Int16, Uint32, Int32, Int64, Float32, Float64
136	function write{T}(f::FITS, data::Array{T};
137	header::Union{Void, FITSHeader}=nothing,
138	name::Union{Void, String}=nothing,
139	ver::Union{Void, Integer}=nothing)
140	fits_assert_open(f.fitsfile)	115×
141	s = size(data)	91×
142	fits_create_img(f.fitsfile, T, [s...])	91×
143	if isa(header, FITSHeader)	111×
144	fits_write_header(f.fitsfile, header, true)	27×
145	end	only 166.1 and 166.4 - 258×
146	if isa(name, String)	117×
UNCOV 147	fits_update_key(f.fitsfile, "EXTNAME", name)	!
148	end
149	if isa(ver, Integer)	117×
UNCOV 150	fits_update_key(f.fitsfile, "EXTVER", ver)	!
151	end
152	fits_write_pix(f.fitsfile, ones(Int, length(s)), length(data), data)	91×
153	nothing	91×
154	end
155
156	# Copy a rectangular section of an image and write it to a new FITS
157	# primary image or image extension. The new image HDU is appended to
158	# the end of the output file; all the keywords in the input image will
159	# be copied to the output image. The common WCS keywords will be
160	# updated if necessary to correspond to the coordinates of the section.
161
162	# convert a range to a string that cfitsio understands
163	cfitsio_range_string(r::UnitRange) = @sprintf "%d:%d" first(r) last(r)	15×
164	cfitsio_range_string(r::StepRange) =	5×
UNCOV 165	@sprintf "%d:%d:%d" first(r) last(r) step(r)	!
166
167	function copy_section(hdu::ImageHDU, dest::FITS, r::Range{Int}...)
168	fits_assert_open(hdu.fitsfile)	10×
169	fits_assert_open(dest.fitsfile)	14×
170	fits_movabs_hdu(hdu.fitsfile, hdu.ext)	14×
171	fits_copy_image_section(hdu.fitsfile, dest.fitsfile,	46×
172	join([cfitsio_range_string(ri) for ri in r], ','))
173	end

JuliaAstro / FITSIO.jl / 166

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