@fideus-labs/ngff-zarr 0.1.0 → 0.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (44) hide show
  1. package/README.md +1 -0
  2. package/esm/io/itk_image_to_ngff_image.d.ts +5 -0
  3. package/esm/io/itk_image_to_ngff_image.d.ts.map +1 -1
  4. package/esm/io/itk_image_to_ngff_image.js +20 -20
  5. package/esm/io/ngff_image_to_itk_image.d.ts.map +1 -1
  6. package/esm/io/ngff_image_to_itk_image.js +2 -0
  7. package/esm/io/to_multiscales.js +1 -1
  8. package/esm/io/to_ngff_zarr.js +16 -0
  9. package/esm/methods/itkwasm.d.ts.map +1 -1
  10. package/esm/methods/itkwasm.js +568 -426
  11. package/esm/schemas/coordinate_systems.d.ts +159 -552
  12. package/esm/schemas/coordinate_systems.d.ts.map +1 -1
  13. package/esm/schemas/coordinate_systems.js +0 -1
  14. package/esm/schemas/ome_zarr.d.ts +105 -69
  15. package/esm/schemas/ome_zarr.d.ts.map +1 -1
  16. package/esm/schemas/rfc4.d.ts +26 -131
  17. package/esm/schemas/rfc4.d.ts.map +1 -1
  18. package/esm/schemas/units.d.ts +70 -5
  19. package/esm/schemas/units.d.ts.map +1 -1
  20. package/esm/schemas/units.js +2 -15
  21. package/esm/schemas/zarr_metadata.d.ts +13 -300
  22. package/esm/schemas/zarr_metadata.d.ts.map +1 -1
  23. package/package.json +1 -1
  24. package/script/io/itk_image_to_ngff_image.d.ts +5 -0
  25. package/script/io/itk_image_to_ngff_image.d.ts.map +1 -1
  26. package/script/io/itk_image_to_ngff_image.js +20 -20
  27. package/script/io/ngff_image_to_itk_image.d.ts.map +1 -1
  28. package/script/io/ngff_image_to_itk_image.js +2 -0
  29. package/script/io/to_multiscales.js +1 -1
  30. package/script/io/to_ngff_zarr.js +16 -0
  31. package/script/methods/itkwasm.d.ts.map +1 -1
  32. package/script/methods/itkwasm.js +567 -425
  33. package/script/schemas/coordinate_systems.d.ts +159 -552
  34. package/script/schemas/coordinate_systems.d.ts.map +1 -1
  35. package/script/schemas/coordinate_systems.js +0 -1
  36. package/script/schemas/ome_zarr.d.ts +105 -69
  37. package/script/schemas/ome_zarr.d.ts.map +1 -1
  38. package/script/schemas/rfc4.d.ts +26 -131
  39. package/script/schemas/rfc4.d.ts.map +1 -1
  40. package/script/schemas/units.d.ts +70 -5
  41. package/script/schemas/units.d.ts.map +1 -1
  42. package/script/schemas/units.js +2 -15
  43. package/script/schemas/zarr_metadata.d.ts +13 -300
  44. package/script/schemas/zarr_metadata.d.ts.map +1 -1
package/esm/schemas/zarr_metadata.d.ts CHANGED
@@ -1,32 +1,12 @@
1
1
  import { z } from "zod";
2
+ import { AxesTypeSchema, SupportedDimsSchema, UnitsSchema } from "./units.js";
3
+ import { AnatomicalOrientationSchema } from "./rfc4.js";
2
4
  export declare const AxisSchema: z.ZodObject<{
3
- name: z.ZodType<unknown, unknown, z.core.$ZodTypeInternals<unknown, unknown>>;
4
- type: z.ZodType<unknown, unknown, z.core.$ZodTypeInternals<unknown, unknown>>;
5
- unit: z.ZodOptional<z.ZodUnion<[z.ZodType<unknown, unknown, z.core.$ZodTypeInternals<unknown, unknown>>, z.ZodType<unknown, unknown, z.core.$ZodTypeInternals<unknown, unknown>>]>>;
6
- orientation: z.ZodOptional<z.ZodObject<{
7
- type: z.ZodLiteral<"anatomical">;
8
- value: z.ZodEnum<{
9
- "left-to-right": "left-to-right";
10
- "right-to-left": "right-to-left";
11
- "anterior-to-posterior": "anterior-to-posterior";
12
- "posterior-to-anterior": "posterior-to-anterior";
13
- "inferior-to-superior": "inferior-to-superior";
14
- "superior-to-inferior": "superior-to-inferior";
15
- "dorsal-to-ventral": "dorsal-to-ventral";
16
- "ventral-to-dorsal": "ventral-to-dorsal";
17
- "dorsal-to-palmar": "dorsal-to-palmar";
18
- "palmar-to-dorsal": "palmar-to-dorsal";
19
- "dorsal-to-plantar": "dorsal-to-plantar";
20
- "plantar-to-dorsal": "plantar-to-dorsal";
21
- "rostral-to-caudal": "rostral-to-caudal";
22
- "caudal-to-rostral": "caudal-to-rostral";
23
- "cranial-to-caudal": "cranial-to-caudal";
24
- "caudal-to-cranial": "caudal-to-cranial";
25
- "proximal-to-distal": "proximal-to-distal";
26
- "distal-to-proximal": "distal-to-proximal";
27
- }>;
28
- }, z.core.$strip>>;
29
- }, z.core.$strip>;
5
+ name: typeof SupportedDimsSchema;
6
+ type: typeof AxesTypeSchema;
7
+ unit: z.ZodOptional<typeof UnitsSchema>;
8
+ orientation: z.ZodOptional<typeof AnatomicalOrientationSchema>;
9
+ }>;
30
10
  export declare const IdentitySchema: z.ZodObject<{
31
11
  type: z.ZodLiteral<"identity">;
32
12
  }>;
@@ -38,274 +18,7 @@ export declare const TranslationSchema: z.ZodObject<{
38
18
  translation: z.ZodArray<z.ZodNumber>;
39
19
  type: z.ZodLiteral<"translation">;
40
20
  }>;
41
- export declare const TransformSchema: z.ZodUnion<readonly [z.ZodObject<{
42
- scale: z.ZodArray<z.ZodNumber>;
43
- type: z.ZodLiteral<"scale">;
44
- }, z.core.$strip>, z.ZodObject<{
45
- translation: z.ZodArray<z.ZodNumber>;
46
- type: z.ZodLiteral<"translation">;
47
- }, z.core.$strip>, z.ZodObject<{
48
- type: z.ZodLiteral<"identity">;
49
- }, z.core.$strip>, z.ZodUnion<readonly [z.ZodObject<{
50
- type: z.ZodLiteral<"identity">;
51
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
52
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
53
- name: z.ZodOptional<z.ZodString>;
54
- }, z.core.$strip>, z.ZodObject<{
55
- type: z.ZodLiteral<"mapAxis">;
56
- mapAxis: z.ZodRecord<z.ZodString, z.ZodString>;
57
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
58
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
59
- name: z.ZodOptional<z.ZodString>;
60
- }, z.core.$strip>, z.ZodObject<{
61
- type: z.ZodLiteral<"translation">;
62
- translation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
63
- path: z.ZodOptional<z.ZodString>;
64
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
65
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
66
- name: z.ZodOptional<z.ZodString>;
67
- }, z.core.$strip>, z.ZodObject<{
68
- type: z.ZodLiteral<"scale">;
69
- scale: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
70
- path: z.ZodOptional<z.ZodString>;
71
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
72
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
73
- name: z.ZodOptional<z.ZodString>;
74
- }, z.core.$strip>, z.ZodObject<{
75
- type: z.ZodLiteral<"affine">;
76
- affine: z.ZodOptional<z.ZodArray<z.ZodArray<z.ZodNumber>>>;
77
- path: z.ZodOptional<z.ZodString>;
78
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
79
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
80
- name: z.ZodOptional<z.ZodString>;
81
- }, z.core.$strip>, z.ZodObject<{
82
- type: z.ZodLiteral<"rotation">;
83
- rotation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
84
- path: z.ZodOptional<z.ZodString>;
85
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
86
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
87
- name: z.ZodOptional<z.ZodString>;
88
- }, z.core.$strip>, z.ZodObject<{
89
- type: z.ZodLiteral<"sequence">;
90
- transformations: z.ZodArray<z.ZodUnion<readonly [z.ZodObject<{
91
- type: z.ZodLiteral<"identity">;
92
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
93
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
94
- name: z.ZodOptional<z.ZodString>;
95
- }, z.core.$strip>, z.ZodObject<{
96
- type: z.ZodLiteral<"mapAxis">;
97
- mapAxis: z.ZodRecord<z.ZodString, z.ZodString>;
98
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
99
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
100
- name: z.ZodOptional<z.ZodString>;
101
- }, z.core.$strip>, z.ZodObject<{
102
- type: z.ZodLiteral<"translation">;
103
- translation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
104
- path: z.ZodOptional<z.ZodString>;
105
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
106
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
107
- name: z.ZodOptional<z.ZodString>;
108
- }, z.core.$strip>, z.ZodObject<{
109
- type: z.ZodLiteral<"scale">;
110
- scale: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
111
- path: z.ZodOptional<z.ZodString>;
112
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
113
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
114
- name: z.ZodOptional<z.ZodString>;
115
- }, z.core.$strip>, z.ZodObject<{
116
- type: z.ZodLiteral<"affine">;
117
- affine: z.ZodOptional<z.ZodArray<z.ZodArray<z.ZodNumber>>>;
118
- path: z.ZodOptional<z.ZodString>;
119
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
120
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
121
- name: z.ZodOptional<z.ZodString>;
122
- }, z.core.$strip>, z.ZodObject<{
123
- type: z.ZodLiteral<"rotation">;
124
- rotation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
125
- path: z.ZodOptional<z.ZodString>;
126
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
127
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
128
- name: z.ZodOptional<z.ZodString>;
129
- }, z.core.$strip>]>>;
130
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
131
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
132
- name: z.ZodOptional<z.ZodString>;
133
- }, z.core.$strip>, z.ZodObject<{
134
- type: z.ZodLiteral<"inverseOf">;
135
- transformation: z.ZodUnion<readonly [z.ZodObject<{
136
- type: z.ZodLiteral<"identity">;
137
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
138
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
139
- name: z.ZodOptional<z.ZodString>;
140
- }, z.core.$strip>, z.ZodObject<{
141
- type: z.ZodLiteral<"mapAxis">;
142
- mapAxis: z.ZodRecord<z.ZodString, z.ZodString>;
143
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
144
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
145
- name: z.ZodOptional<z.ZodString>;
146
- }, z.core.$strip>, z.ZodObject<{
147
- type: z.ZodLiteral<"translation">;
148
- translation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
149
- path: z.ZodOptional<z.ZodString>;
150
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
151
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
152
- name: z.ZodOptional<z.ZodString>;
153
- }, z.core.$strip>, z.ZodObject<{
154
- type: z.ZodLiteral<"scale">;
155
- scale: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
156
- path: z.ZodOptional<z.ZodString>;
157
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
158
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
159
- name: z.ZodOptional<z.ZodString>;
160
- }, z.core.$strip>, z.ZodObject<{
161
- type: z.ZodLiteral<"affine">;
162
- affine: z.ZodOptional<z.ZodArray<z.ZodArray<z.ZodNumber>>>;
163
- path: z.ZodOptional<z.ZodString>;
164
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
165
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
166
- name: z.ZodOptional<z.ZodString>;
167
- }, z.core.$strip>, z.ZodObject<{
168
- type: z.ZodLiteral<"rotation">;
169
- rotation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
170
- path: z.ZodOptional<z.ZodString>;
171
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
172
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
173
- name: z.ZodOptional<z.ZodString>;
174
- }, z.core.$strip>]>;
175
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
176
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
177
- name: z.ZodOptional<z.ZodString>;
178
- }, z.core.$strip>, z.ZodObject<{
179
- type: z.ZodLiteral<"bijection">;
180
- forward: z.ZodUnion<readonly [z.ZodObject<{
181
- type: z.ZodLiteral<"identity">;
182
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
183
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
184
- name: z.ZodOptional<z.ZodString>;
185
- }, z.core.$strip>, z.ZodObject<{
186
- type: z.ZodLiteral<"mapAxis">;
187
- mapAxis: z.ZodRecord<z.ZodString, z.ZodString>;
188
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
189
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
190
- name: z.ZodOptional<z.ZodString>;
191
- }, z.core.$strip>, z.ZodObject<{
192
- type: z.ZodLiteral<"translation">;
193
- translation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
194
- path: z.ZodOptional<z.ZodString>;
195
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
196
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
197
- name: z.ZodOptional<z.ZodString>;
198
- }, z.core.$strip>, z.ZodObject<{
199
- type: z.ZodLiteral<"scale">;
200
- scale: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
201
- path: z.ZodOptional<z.ZodString>;
202
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
203
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
204
- name: z.ZodOptional<z.ZodString>;
205
- }, z.core.$strip>, z.ZodObject<{
206
- type: z.ZodLiteral<"affine">;
207
- affine: z.ZodOptional<z.ZodArray<z.ZodArray<z.ZodNumber>>>;
208
- path: z.ZodOptional<z.ZodString>;
209
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
210
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
211
- name: z.ZodOptional<z.ZodString>;
212
- }, z.core.$strip>, z.ZodObject<{
213
- type: z.ZodLiteral<"rotation">;
214
- rotation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
215
- path: z.ZodOptional<z.ZodString>;
216
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
217
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
218
- name: z.ZodOptional<z.ZodString>;
219
- }, z.core.$strip>]>;
220
- inverse: z.ZodUnion<readonly [z.ZodObject<{
221
- type: z.ZodLiteral<"identity">;
222
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
223
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
224
- name: z.ZodOptional<z.ZodString>;
225
- }, z.core.$strip>, z.ZodObject<{
226
- type: z.ZodLiteral<"mapAxis">;
227
- mapAxis: z.ZodRecord<z.ZodString, z.ZodString>;
228
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
229
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
230
- name: z.ZodOptional<z.ZodString>;
231
- }, z.core.$strip>, z.ZodObject<{
232
- type: z.ZodLiteral<"translation">;
233
- translation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
234
- path: z.ZodOptional<z.ZodString>;
235
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
236
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
237
- name: z.ZodOptional<z.ZodString>;
238
- }, z.core.$strip>, z.ZodObject<{
239
- type: z.ZodLiteral<"scale">;
240
- scale: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
241
- path: z.ZodOptional<z.ZodString>;
242
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
243
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
244
- name: z.ZodOptional<z.ZodString>;
245
- }, z.core.$strip>, z.ZodObject<{
246
- type: z.ZodLiteral<"affine">;
247
- affine: z.ZodOptional<z.ZodArray<z.ZodArray<z.ZodNumber>>>;
248
- path: z.ZodOptional<z.ZodString>;
249
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
250
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
251
- name: z.ZodOptional<z.ZodString>;
252
- }, z.core.$strip>, z.ZodObject<{
253
- type: z.ZodLiteral<"rotation">;
254
- rotation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
255
- path: z.ZodOptional<z.ZodString>;
256
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
257
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
258
- name: z.ZodOptional<z.ZodString>;
259
- }, z.core.$strip>]>;
260
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
261
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
262
- name: z.ZodOptional<z.ZodString>;
263
- }, z.core.$strip>, z.ZodObject<{
264
- type: z.ZodLiteral<"byDimension">;
265
- transformations: z.ZodArray<z.ZodUnion<readonly [z.ZodObject<{
266
- type: z.ZodLiteral<"identity">;
267
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
268
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
269
- name: z.ZodOptional<z.ZodString>;
270
- }, z.core.$strip>, z.ZodObject<{
271
- type: z.ZodLiteral<"mapAxis">;
272
- mapAxis: z.ZodRecord<z.ZodString, z.ZodString>;
273
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
274
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
275
- name: z.ZodOptional<z.ZodString>;
276
- }, z.core.$strip>, z.ZodObject<{
277
- type: z.ZodLiteral<"translation">;
278
- translation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
279
- path: z.ZodOptional<z.ZodString>;
280
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
281
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
282
- name: z.ZodOptional<z.ZodString>;
283
- }, z.core.$strip>, z.ZodObject<{
284
- type: z.ZodLiteral<"scale">;
285
- scale: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
286
- path: z.ZodOptional<z.ZodString>;
287
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
288
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
289
- name: z.ZodOptional<z.ZodString>;
290
- }, z.core.$strip>, z.ZodObject<{
291
- type: z.ZodLiteral<"affine">;
292
- affine: z.ZodOptional<z.ZodArray<z.ZodArray<z.ZodNumber>>>;
293
- path: z.ZodOptional<z.ZodString>;
294
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
295
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
296
- name: z.ZodOptional<z.ZodString>;
297
- }, z.core.$strip>, z.ZodObject<{
298
- type: z.ZodLiteral<"rotation">;
299
- rotation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
300
- path: z.ZodOptional<z.ZodString>;
301
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
302
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
303
- name: z.ZodOptional<z.ZodString>;
304
- }, z.core.$strip>]>>;
305
- input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
306
- output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
307
- name: z.ZodOptional<z.ZodString>;
308
- }, z.core.$strip>]>]>;
21
+ export declare const TransformSchema: z.ZodType<unknown>;
309
22
  export declare const DatasetSchema: z.ZodObject<{
310
23
  path: z.ZodString;
311
24
  coordinateTransformations: z.ZodArray<typeof TransformSchema>;
@@ -324,11 +37,11 @@ export declare const OmeroChannelSchema: z.ZodObject<{
324
37
  export declare const OmeroSchema: z.ZodObject<{
325
38
  channels: z.ZodArray<typeof OmeroChannelSchema>;
326
39
  }>;
327
- export declare const MethodMetadataSchema: z.ZodObject<{
328
- description: z.ZodString;
329
- method: z.ZodString;
330
- version: z.ZodString;
331
- }, z.core.$strip>;
40
+ export declare const MethodMetadataSchema: z.ZodType<{
41
+ description: string;
42
+ method: string;
43
+ version: string;
44
+ }>;
332
45
  export declare const MetadataSchema: z.ZodObject<{
333
46
  axes: z.ZodArray<typeof AxisSchema>;
334
47
  datasets: z.ZodArray<typeof DatasetSchema>;
package/esm/schemas/zarr_metadata.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"zarr_metadata.d.ts","sourceRoot":"","sources":["../../src/schemas/zarr_metadata.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAMxB,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAMrB,CAAC;AAGH,eAAO,MAAM,cAAc,EAAE,CAAC,CAAC,SAAS,CAAC;IACvC,IAAI,EAAE,CAAC,CAAC,UAAU,CAAC,UAAU,CAAC,CAAC;CAChC,CAEC,CAAC;AAEH,eAAO,MAAM,WAAW,EAAE,CAAC,CAAC,SAAS,CAAC;IACpC,KAAK,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IAC/B,IAAI,EAAE,CAAC,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC;CAC7B,CAGC,CAAC;AAEH,eAAO,MAAM,iBAAiB,EAAE,CAAC,CAAC,SAAS,CAAC;IAC1C,WAAW,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IACrC,IAAI,EAAE,CAAC,CAAC,UAAU,CAAC,aAAa,CAAC,CAAC;CACnC,CAGC,CAAC;AAGH,eAAO,MAAM,eAAe;WAhBnB,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC;UACxB,CAAC,CAAC,UAAU,CAAC,OAAO,CAAC;;iBAOd,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC;UAC9B,CAAC,CAAC,UAAU,CAAC,aAAa,CAAC;;UAf3B,CAAC,CAAC,UAAU,CAAC,UAAU,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBA2B9B,CAAC;AAEH,eAAO,MAAM,aAAa,EAAE,CAAC,CAAC,SAAS,CAAC;IACtC,IAAI,EAAE,CAAC,CAAC,SAAS,CAAC;IAClB,yBAAyB,EAAE,CAAC,CAAC,QAAQ,CAAC,OAAO,eAAe,CAAC,CAAC;CAC/D,CAGC,CAAC;AAEH,eAAO,MAAM,iBAAiB,EAAE,CAAC,CAAC,SAAS,CAAC;IAC1C,GAAG,EAAE,CAAC,CAAC,SAAS,CAAC;IACjB,GAAG,EAAE,CAAC,CAAC,SAAS,CAAC;IACjB,KAAK,EAAE,CAAC,CAAC,SAAS,CAAC;IACnB,GAAG,EAAE,CAAC,CAAC,SAAS,CAAC;CAClB,CAKC,CAAC;AAEH,eAAO,MAAM,kBAAkB,EAAE,CAAC,CAAC,SAAS,CAAC;IAC3C,KAAK,EAAE,CAAC,CAAC,SAAS,CAAC;IACnB,MAAM,EAAE,OAAO,iBAAiB,CAAC;IACjC,KAAK,EAAE,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;CACnC,CAMC,CAAC;AAEH,eAAO,MAAM,WAAW,EAAE,CAAC,CAAC,SAAS,CAAC;IACpC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,OAAO,kBAAkB,CAAC,CAAC;CACjD,CAEC,CAAC;AAEH,eAAO,MAAM,oBAAoB;;;;iBAI/B,CAAC;AAEH,eAAO,MAAM,cAAc,EAAE,CAAC,CAAC,SAAS,CAAC;IACvC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAC,OAAO,UAAU,CAAC,CAAC;IACpC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,OAAO,aAAa,CAAC,CAAC;IAC3C,yBAAyB,EAAE,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,QAAQ,CAAC,OAAO,eAAe,CAAC,CAAC,CAAC;IAC7E,KAAK,EAAE,CAAC,CAAC,WAAW,CAAC,OAAO,WAAW,CAAC,CAAC;IACzC,IAAI,EAAE,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IAChC,OAAO,EAAE,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IACnC,IAAI,EAAE,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IACjC,QAAQ,EAAE,CAAC,CAAC,WAAW,CAAC,OAAO,oBAAoB,CAAC,CAAC;CACtD,CASC,CAAC"}
1
+ {"version":3,"file":"zarr_metadata.d.ts","sourceRoot":"","sources":["../../src/schemas/zarr_metadata.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AACxB,OAAO,EAAE,cAAc,EAAE,mBAAmB,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AAC9E,OAAO,EAAE,2BAA2B,EAAE,MAAM,WAAW,CAAC;AAIxD,eAAO,MAAM,UAAU,EAAE,CAAC,CAAC,SAAS,CAAC;IACnC,IAAI,EAAE,OAAO,mBAAmB,CAAC;IACjC,IAAI,EAAE,OAAO,cAAc,CAAC;IAC5B,IAAI,EAAE,CAAC,CAAC,WAAW,CAAC,OAAO,WAAW,CAAC,CAAC;IACxC,WAAW,EAAE,CAAC,CAAC,WAAW,CAAC,OAAO,2BAA2B,CAAC,CAAC;CAChE,CAMC,CAAC;AAGH,eAAO,MAAM,cAAc,EAAE,CAAC,CAAC,SAAS,CAAC;IACvC,IAAI,EAAE,CAAC,CAAC,UAAU,CAAC,UAAU,CAAC,CAAC;CAChC,CAEC,CAAC;AAEH,eAAO,MAAM,WAAW,EAAE,CAAC,CAAC,SAAS,CAAC;IACpC,KAAK,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IAC/B,IAAI,EAAE,CAAC,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC;CAC7B,CAGC,CAAC;AAEH,eAAO,MAAM,iBAAiB,EAAE,CAAC,CAAC,SAAS,CAAC;IAC1C,WAAW,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IACrC,IAAI,EAAE,CAAC,CAAC,UAAU,CAAC,aAAa,CAAC,CAAC;CACnC,CAGC,CAAC;AAGH,eAAO,MAAM,eAAe,EAAE,CAAC,CAAC,OAAO,CAAC,OAAO,CAK7C,CAAC;AAEH,eAAO,MAAM,aAAa,EAAE,CAAC,CAAC,SAAS,CAAC;IACtC,IAAI,EAAE,CAAC,CAAC,SAAS,CAAC;IAClB,yBAAyB,EAAE,CAAC,CAAC,QAAQ,CAAC,OAAO,eAAe,CAAC,CAAC;CAC/D,CAGC,CAAC;AAEH,eAAO,MAAM,iBAAiB,EAAE,CAAC,CAAC,SAAS,CAAC;IAC1C,GAAG,EAAE,CAAC,CAAC,SAAS,CAAC;IACjB,GAAG,EAAE,CAAC,CAAC,SAAS,CAAC;IACjB,KAAK,EAAE,CAAC,CAAC,SAAS,CAAC;IACnB,GAAG,EAAE,CAAC,CAAC,SAAS,CAAC;CAClB,CAKC,CAAC;AAEH,eAAO,MAAM,kBAAkB,EAAE,CAAC,CAAC,SAAS,CAAC;IAC3C,KAAK,EAAE,CAAC,CAAC,SAAS,CAAC;IACnB,MAAM,EAAE,OAAO,iBAAiB,CAAC;IACjC,KAAK,EAAE,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;CACnC,CAMC,CAAC;AAEH,eAAO,MAAM,WAAW,EAAE,CAAC,CAAC,SAAS,CAAC;IACpC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,OAAO,kBAAkB,CAAC,CAAC;CACjD,CAEC,CAAC;AAEH,eAAO,MAAM,oBAAoB,EAAE,CAAC,CAAC,OAAO,CAAC;IAC3C,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,EAAE,MAAM,CAAC;CACjB,CAIC,CAAC;AAEH,eAAO,MAAM,cAAc,EAAE,CAAC,CAAC,SAAS,CAAC;IACvC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAC,OAAO,UAAU,CAAC,CAAC;IACpC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,OAAO,aAAa,CAAC,CAAC;IAC3C,yBAAyB,EAAE,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,QAAQ,CAAC,OAAO,eAAe,CAAC,CAAC,CAAC;IAC7E,KAAK,EAAE,CAAC,CAAC,WAAW,CAAC,OAAO,WAAW,CAAC,CAAC;IACzC,IAAI,EAAE,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IAChC,OAAO,EAAE,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IACnC,IAAI,EAAE,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IACjC,QAAQ,EAAE,CAAC,CAAC,WAAW,CAAC,OAAO,oBAAoB,CAAC,CAAC;CACtD,CASC,CAAC"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@fideus-labs/ngff-zarr",
3
- "version": "0.1.0",
3
+ "version": "0.2.0",
4
4
  "description": "TypeScript implementation of ngff-zarr for reading and writing OME-Zarr files",
5
5
  "keywords": [
6
6
  "ome-zarr",
package/script/io/itk_image_to_ngff_image.d.ts CHANGED
@@ -9,6 +9,11 @@ export interface ItkImageToNgffImageOptions {
9
9
  * @default true
10
10
  */
11
11
  addAnatomicalOrientation?: boolean;
12
+ /**
13
+ * Path prefix for the zarr array (e.g., "scale0/", "scale1/")
14
+ * @default "image"
15
+ */
16
+ path?: string;
12
17
  }
13
18
  /**
14
19
  * Convert an ITK-Wasm Image to an NgffImage, preserving spatial metadata.
package/script/io/itk_image_to_ngff_image.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"itk_image_to_ngff_image.d.ts","sourceRoot":"","sources":["../../src/io/itk_image_to_ngff_image.ts"],"names":[],"mappings":"AAEA;;GAEG;AAEH,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,UAAU,CAAC;AAEtC,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAOnD,MAAM,WAAW,0BAA0B;IACzC;;;OAGG;IACH,wBAAwB,CAAC,EAAE,OAAO,CAAC;CACpC;AAED;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,QAAQ,EAAE,KAAK,EACf,OAAO,GAAE,0BAA+B,GACvC,OAAO,CAAC,SAAS,CAAC,CAmHpB"}
1
+ {"version":3,"file":"itk_image_to_ngff_image.d.ts","sourceRoot":"","sources":["../../src/io/itk_image_to_ngff_image.ts"],"names":[],"mappings":"AAEA;;GAEG;AAEH,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,UAAU,CAAC;AAEtC,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAOnD,MAAM,WAAW,0BAA0B;IACzC;;;OAGG;IACH,wBAAwB,CAAC,EAAE,OAAO,CAAC;IAEnC;;;OAGG;IACH,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,QAAQ,EAAE,KAAK,EACf,OAAO,GAAE,0BAA+B,GACvC,OAAO,CAAC,SAAS,CAAC,CAmHpB"}
package/script/io/itk_image_to_ngff_image.js CHANGED
@@ -46,10 +46,12 @@ const zarrita_1 = require("zarrita");
46
46
  * @returns Promise resolving to NgffImage
47
47
  */
48
48
  async function itkImageToNgffImage(itkImage, options = {}) {
49
- const { addAnatomicalOrientation = true } = options;
49
+ const { addAnatomicalOrientation = true, path = "image" } = options;
50
50
  // Extract image properties from ITK-Wasm Image
51
51
  const _data = itkImage.data;
52
- const shape = itkImage.size;
52
+ // ITK stores size in physical space order [x, y, z], but the data buffer is in
53
+ // C-order (row-major) which means [z, y, x] indexing. Reverse to match data layout.
54
+ const shape = [...itkImage.size].reverse();
53
55
  const spacing = itkImage.spacing;
54
56
  const origin = itkImage.origin;
55
57
  const ndim = shape.length;
@@ -86,32 +88,27 @@ async function itkImageToNgffImage(itkImage, options = {}) {
86
88
  // Identify spatial dimensions
87
89
  const allSpatialDims = new Set(["x", "y", "z"]);
88
90
  const spatialDims = dims.filter((dim) => allSpatialDims.has(dim));
89
- // Create scale mapping from spacing (ITK order: [z, y, x] for 3D, [y, x] for 2D)
91
+ // Create scale mapping from spacing
92
+ // ITK stores spacing/origin in physical space order (x, y, z),
93
+ // but we need to map them to array order (z, y, x).
94
+ // Reverse the arrays to convert from physical to array order, matching Python implementation.
90
95
  const scale = {};
91
- // Define canonical ITK spatial order for up to 3D
92
- const itkSpatialOrder = ["z", "y", "x"].slice(-spatialDims.length);
93
- spatialDims.forEach((dim) => {
94
- const spatialIndex = itkSpatialOrder.indexOf(dim);
95
- if (spatialIndex === -1) {
96
- throw new Error(`Unknown spatial dimension: ${dim}`);
97
- }
98
- scale[dim] = spacing[spatialIndex];
96
+ const reversedSpacing = spacing.slice().reverse();
97
+ spatialDims.forEach((dim, idx) => {
98
+ scale[dim] = reversedSpacing[idx];
99
99
  });
100
- // Create translation mapping from origin (ITK order: [z, y, x] for 3D, [y, x] for 2D)
100
+ // Create translation mapping from origin
101
101
  const translation = {};
102
- spatialDims.forEach((dim) => {
103
- const spatialIndex = itkSpatialOrder.indexOf(dim);
104
- if (spatialIndex === -1) {
105
- throw new Error(`Unknown spatial dimension: ${dim}`);
106
- }
107
- translation[dim] = origin[spatialIndex];
102
+ const reversedOrigin = origin.slice().reverse();
103
+ spatialDims.forEach((dim, idx) => {
104
+ translation[dim] = reversedOrigin[idx];
108
105
  });
109
106
  // Create Zarr array from ITK-Wasm data
110
107
  const store = new Map();
111
108
  const root = zarr.root(store);
112
109
  // Determine appropriate chunk size
113
110
  const chunkShape = shape.map((s) => Math.min(s, 256));
114
- const zarrArray = await zarr.create(root.resolve("image"), {
111
+ const zarrArray = await zarr.create(root.resolve(path), {
115
112
  shape: shape,
116
113
  chunk_shape: chunkShape,
117
114
  data_type: imageType.componentType,
@@ -122,10 +119,13 @@ async function itkImageToNgffImage(itkImage, options = {}) {
122
119
  // Create a selection that covers the entire array (null means "all" for each dimension)
123
120
  const selection = new Array(ndim).fill(null);
124
121
  // Create a chunk object with the ITK-Wasm data in zarrita format
122
+ // ITK-Wasm stores data in column-major order with size [x, y, z],
123
+ // which has the same memory layout as C-order (row-major) with shape [z, y, x].
124
+ // We reversed the shape above, and now use C-order strides for that reversed shape.
125
125
  const dataChunk = {
126
126
  data: itkImage.data,
127
127
  shape: shape,
128
- stride: (0, zarrita_1._zarrita_internal_get_strides)(shape, "C"), // C-order (row-major) strides for compatibility
128
+ stride: (0, zarrita_1._zarrita_internal_get_strides)(shape, "C"), // C-order strides for the reversed shape
129
129
  };
130
130
  // Write all data to the zarr array using zarrita's set function
131
131
  // This handles chunking and encoding automatically
package/script/io/ngff_image_to_itk_image.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"ngff_image_to_itk_image.d.ts","sourceRoot":"","sources":["../../src/io/ngff_image_to_itk_image.ts"],"names":[],"mappings":"AAEA;;GAEG;AAEH,OAAO,KAAK,EAEV,KAAK,EAKN,MAAM,UAAU,CAAC;AAElB,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAEnD,MAAM,WAAW,0BAA0B;IACzC;;;OAGG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC;IAEhB;;;OAGG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAsED;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,SAAS,EAAE,SAAS,EACpB,OAAO,GAAE,0BAA+B,GACvC,OAAO,CAAC,KAAK,CAAC,CAiMhB"}
1
+ {"version":3,"file":"ngff_image_to_itk_image.d.ts","sourceRoot":"","sources":["../../src/io/ngff_image_to_itk_image.ts"],"names":[],"mappings":"AAEA;;GAEG;AAEH,OAAO,KAAK,EAEV,KAAK,EAKN,MAAM,UAAU,CAAC;AAElB,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAEnD,MAAM,WAAW,0BAA0B;IACzC;;;OAGG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC;IAEhB;;;OAGG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAsED;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,SAAS,EAAE,SAAS,EACpB,OAAO,GAAE,0BAA+B,GACvC,OAAO,CAAC,KAAK,CAAC,CAmMhB"}
package/script/io/ngff_image_to_itk_image.js CHANGED
@@ -194,6 +194,8 @@ async function ngffImageToItkImage(ngffImage, options = {}) {
194
194
  return order.indexOf(a) - order.indexOf(b);
195
195
  });
196
196
  // Create ITK spacing, origin, and size arrays
197
+ // sortedItkDims is already in physical space order [x, y, z]
198
+ // Mapping from dims extracts the correct values from NGFF's array order [z, y, x]
197
199
  const spacing = sortedItkDims.map((dim) => workingImage.scale[dim] || 1.0);
198
200
  const origin = sortedItkDims.map((dim) => workingImage.translation[dim] || 0.0);
199
201
  const size = sortedItkDims.map((dim) => data.shape[dims.indexOf(dim)]);
package/script/io/to_multiscales.js CHANGED
@@ -52,7 +52,7 @@ async function toMultiscales(image, options = {}) {
52
52
  });
53
53
  // Create datasets for all images
54
54
  const datasets = images.map((img, index) => {
55
- return (0, factory_js_1.createDataset)(`${index}`, img.dims.map((dim) => img.scale[dim]), img.dims.map((dim) => img.translation[dim]));
55
+ return (0, factory_js_1.createDataset)(`scale${index}`, img.dims.map((dim) => img.scale[dim]), img.dims.map((dim) => img.translation[dim]));
56
56
  });
57
57
  // Create metadata with method information
58
58
  const methodMetadata = (0, method_metadata_js_1.getMethodMetadata)(method);
package/script/io/to_ngff_zarr.js CHANGED
@@ -220,6 +220,22 @@ async function writeChunkWithGet(zarrArray, image, chunkIndex) {
220
220
  // Convert chunk data to target type
221
221
  const targetTypedArrayConstructor = getTypedArrayConstructor(zarrArray.dtype);
222
222
  const chunkTargetData = convertChunkToTargetType(chunkSourceData, zarrArray.dtype, targetTypedArrayConstructor);
223
+ // Validate chunk data size
224
+ const expectedSize = chunkShape.reduce((a, b) => a * b, 1);
225
+ const actualSize = chunkTargetData.byteLength /
226
+ (chunkTargetData
227
+ .BYTES_PER_ELEMENT || 1);
228
+ if (actualSize !== expectedSize) {
229
+ console.error(`[writeChunkWithGet] Chunk data size mismatch!`);
230
+ console.error(` Image shape:`, shape);
231
+ console.error(` Chunk index:`, chunkIndex);
232
+ console.error(` Chunk start:`, chunkStart);
233
+ console.error(` Chunk end:`, chunkEnd);
234
+ console.error(` Chunk shape:`, chunkShape);
235
+ console.error(` Expected size:`, expectedSize);
236
+ console.error(` Actual size:`, actualSize);
237
+ throw new Error(`Chunk data size mismatch: expected ${expectedSize} elements, got ${actualSize}`);
238
+ }
223
239
  // Create the selection for writing to the target zarr array
224
240
  const targetSelection = chunkStart.map((start, dim) => zarr.slice(start, chunkEnd[dim]));
225
241
  // Write the chunk using zarrita's set function
package/script/methods/itkwasm.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"itkwasm.d.ts","sourceRoot":"","sources":["../../src/methods/itkwasm.ts"],"names":[],"mappings":"AAeA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAohCnD;;GAEG;AACH,wBAAsB,iBAAiB,CACrC,SAAS,EAAE,SAAS,EACpB,YAAY,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,EACjD,SAAS,EAAE,UAAU,GAAG,YAAY,GAAG,aAAa,GACnD,OAAO,CAAC,SAAS,EAAE,CAAC,CA+CtB"}
1
+ {"version":3,"file":"itkwasm.d.ts","sourceRoot":"","sources":["../../src/methods/itkwasm.ts"],"names":[],"mappings":"AAcA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAknCnD;;GAEG;AACH,wBAAsB,iBAAiB,CACrC,SAAS,EAAE,SAAS,EACpB,YAAY,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,EACjD,SAAS,EAAE,UAAU,GAAG,YAAY,GAAG,aAAa,GACnD,OAAO,CAAC,SAAS,EAAE,CAAC,CA8HtB"}