1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
|
module Images
import ..CrystFEL: libcrystfel
import ..CrystFEL.DataTemplates: DataTemplate, InternalDataTemplate
import ..CrystFEL.DetGeoms: DetGeom
import ..CrystFEL.PeakLists: PeakList, InternalPeakList
import ..CrystFEL.Crystals: Crystal, InternalCrystal
export Image
const HEADER_CACHE_SIZE = 128
mutable struct InternalImage
dp::Ptr{Ptr{Cfloat}}
bad::Ptr{Ptr{Cint}}
sat::Ptr{Ptr{Cfloat}}
hit::Cint
crystals::Ptr{Ptr{Cvoid}}
n_crystals::Cint
indexed_by::Cint
n_indexing_tries::Cint
detgeom::Ptr{DetGeom}
data_source_type::Cint
filename::Cstring
ev::Cstring
data_block::Ptr{Cvoid}
data_block_size::Csize_t
meta_data::Cstring
header_cache::NTuple{HEADER_CACHE_SIZE, Ptr{Cvoid}}
n_cached_headers::Cint
id::Cint
serial::Cint
spectrum::Ptr{Cvoid}
lambda::Cdouble
div::Cdouble
bw::Cdouble
peak_resolution::Cdouble
peaklist::Ptr{InternalPeakList}
ida::Ptr{Cvoid}
owns_peaklist::Cint
end
mutable struct Image
internalptr::Ptr{InternalImage}
peaklist::Union{Nothing,PeakList}
end
function makecrystallist(listptr, n)
crystals = Crystal[]
if listptr == C_NULL
return crystals
end
for i in 1:n
crystalptr = unsafe_load(listptr, i)
push!(crystals, Crystal(crystalptr, true))
end
crystals
end
function getpeaklist(image)
idata = unsafe_load(image.internalptr)
if (image.peaklist === nothing) || (idata.peaklist != image.peaklist.internalptr)
if idata.peaklist != C_NULL
image.peaklist = PeakList(idata.peaklist)
# From now on, Julia is completely responsible for freeing the peaklist
idata.owns_peaklist = 0
unsafe_store!(image.internalptr, idata)
else
image.peaklist = nothing
end
end
return image.peaklist
end
function Base.getproperty(image::Image, name::Symbol)
if name === :internalptr
getfield(image, :internalptr)
elseif name === :peaklist
getpeaklist(image)
else
idata = unsafe_load(image.internalptr)
if name === :crystals
return makecrystallist(getproperty(idata, :crystals),
getproperty(idata, :n_crystals))
else
getproperty(idata, name)
end
end
end
strdup(str) = @ccall strdup(str::Cstring)::Cstring
function assert_type(val, type)
if !(val isa type)
throw(ArgumentError("Must be a "*string(type)*" (have "*string(typeof(val))*" instead)"))
end
end
function set_peaklist(image, new_pl)
assert_type(new_pl, PeakList)
idata = unsafe_load(image.internalptr)
if (idata.owns_peaklist == 0) && (idata.peaklist != C_NULL)
@ccall libcrystfel.image_feature_list_free(idata.peaklist::Ptr{InternalPeakList})::Cvoid
end
idata.peaklist = new_pl.internalptr
idata.owns_peaklist = 0
unsafe_store!(image.internalptr, idata)
end
function Base.setproperty!(image::Image, name::Symbol, val)
if name === :internalptr
setfield!(image, :internalptr, val)
else
if name === :peaklist
return set_peaklist(image, val)
elseif name === :filename
assert_type(val, AbstractString)
val = strdup(val)
elseif name === :ev
assert_type(val, AbstractString)
val = strdup(val)
end
idata = unsafe_load(image.internalptr)
setproperty!(idata, name, val)
unsafe_store!(image.internalptr, idata)
end
end
function Base.propertynames(image::Image; private=false)
if private
fieldnames(InternalImage)
else
tuple(fieldnames(InternalImage)..., :internalptr)
end
end
function Base.push!(image::Image, cr::Crystal)
if cr.in_image
throw(ErrorException("Crystal is already in an image"))
end
ccall((:image_add_crystal, libcrystfel),
Cvoid, (Ptr{InternalImage},Ptr{InternalCrystal}),
image.internalptr, cr.internalptr)
cr.in_image = true
end
"""
Image(dtempl::DataTemplate)
Creates a CrystFEL image structure, not linked to any file or data block,
i.e. for simulation purposes. This will fail if `dtempl` contains any
references to metadata fields, e.g. `photon_energy = /LCLS/photon_energy eV`.
Corresponds to CrystFEL C API function `image_create_for_simulation()`.
"""
function Image(dtempl::DataTemplate)
out = ccall((:image_create_for_simulation, libcrystfel),
Ptr{Image}, (Ref{InternalDataTemplate},), dtempl.internalptr)
if out == C_NULL
throw(ArgumentError("Failed to create image"))
end
image = Image(out, nothing)
finalizer(image) do x
ccall((:image_free, libcrystfel), Cvoid, (Ptr{InternalImage},), x.internalptr)
end
return image
end
"""
Image(dtempl::DataTemplate, filename::AbstractString, event::AbstractString,
no_image_data=false, no_mask_data=false)
Loads an image from the filesystem.
Corresponds to CrystFEL C API function `image_read()`.
"""
function Image(dtempl::DataTemplate,
filename::AbstractString,
event::AbstractString="//",
no_image_data=false,
no_mask_data=false)
out = @ccall libcrystfel.image_read(dtempl.internalptr::Ptr{InternalDataTemplate},
filename::Cstring, event::Cstring,
no_image_data::Cint, no_mask_data::Cint,
C_NULL::Ptr{Cvoid})::Ptr{Image}
if out == C_NULL
throw(ArgumentError("Failed to load image"))
end
image = Image(out, nothing)
finalizer(image) do x
ccall((:image_free, libcrystfel), Cvoid, (Ptr{InternalImage},), x.internalptr)
end
return image
end
end # of module
|
