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Issue with LoadVizgen #8597

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angie-john opened this issue Mar 8, 2024 · 14 comments
Open

Issue with LoadVizgen #8597

angie-john opened this issue Mar 8, 2024 · 14 comments

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@angie-john
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I'm trying to follow this tutorial: https://satijalab.org/seurat/articles/seurat5_spatial_vignette_2 but I'm unable to properly load the data. I'm having the same issue as #7142 however, I'm unable to fix it like they did. I believe I have the data downloaded and named correctly.
This is the error I get:
image

This is my session info:
image

These are what my files look like:
image
image

I would greatly appreciate any help with this.
@alikhuseynov
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I'm not from Seurat dev team.. however, It is related to future library. Try to install this PR (still under review) I did for updated Vizgen output

  • Support to handle .parquet output from Vizgen #7190
    remotes::install_github(repo = 'alikhuseynov/vizgen_seurat5', ref = 'feat/vizgen') # for Seurat/SeuratObject v5
    remotes::install_github(repo = 'alikhuseynov/seurat', ref = 'feat/vizgen') # for Seurat/SeuratObject v4

Here is an example on how to use that optimized function. Instead of using future, use BiocParallel and set the cores within LoadVizgen(use.BiocParallel = TRUE, workers.MulticoreParam = 4) that should work.

@angie-john
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I tried to do what you suggested but received these errors. I believe I had installed the packages correctly though.

vizgen error biocparallel

@alikhuseynov
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I tried to do what you suggested but received these errors. I believe I had installed the packages correctly though.

vizgen error biocparallel

I don't think it uses the optimized LoadVizgen since it tells you that there are unused arguments

@angie-john
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Hm.. do you know how I would use the optimized LoadVizgen instead?

@alikhuseynov
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Hm.. do you know how I would use the optimized LoadVizgen instead?

You didn't install that PR on Vizgen properly. After install restart your R session, then it should work.

@angie-john
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I was able to get that to work but I'm still getting the issue with the future library

error cannot ffind HDF5 file
Do you have any other suggestions for what could fix it? Greatly appreciate your help so far.

@groverj3
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groverj3 commented Apr 5, 2024

Adding my voice to the choir of users who have run into this issue while testing Seurat's suitability for our spatial transcriptomics experiments.

I was able to get data loaded using @alikhuseynov 's PR. Hopefully this is incorporated into Seurat in a future update.

@alikhuseynov
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alikhuseynov commented Apr 5, 2024 •
edited

I was able to get that to work but I'm still getting the issue with the future library

error cannot ffind HDF5 file

Do you have any other suggestions for what could fix it? Greatly appreciate your help so far.

Did it work to make the final object then?
And don't use plan("multisession", workers = 10) before loading the object

@angie-john
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Yes I was able to make the object but it was unable to read the hdf5 files still.

@alikhuseynov
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Yes I was able to make the object but it was unable to read the hdf5 files still.

did it read any hdf5 files at all or just didn't read some?
it is hard to debug like this and I'm not working on windows machine.
Please provide your code or at least final output of function run, and how the object looks like, does it have any FOV etc..?
also add sessionInfo(), not just screenshots, one cannot see anything there.
and avoid using whitespaces in directory names like mouse brain vizgen data, use _ instead.

@angie-john
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It wasn't able to read any of the hdf5 files.
This is my code:

library(Seurat)
library(ggplot2)
library(data.table)
library(hdf5r)
library(dplyr)
library(BiocParallel)
library(magrittr)
library(progressr)
library(sf)


vizgen.obj <- LoadVizgen(data.dir = "C:/Users/gangliagurdian/Documents/practice/mouse_brain_vizgen_data", 
                        fov = "s2r1", 
                        use.BiocParallel = TRUE,
                        verbose = TRUE,
                        workers.MulticoreParam = 4 ) 
vizgen.obj <- SCTransform(vizgen.obj, assay = "Vizgen", clip.range = c(-10, 10))
vizgen.obj <- RunPCA(vizgen.obj, npcs = 30, features = rownames(vizgen.obj))
vizgen.obj <- RunUMAP(vizgen.obj, dims = 1:30)
vizgen.obj <- FindNeighbors(vizgen.obj, reduction = "pca", dims = 1:30)
vizgen.obj <- FindClusters(vizgen.obj, resolution = 0.3)

DimPlot(vizgen.obj, reduction = "umap")
ImageDimPlot(vizgen.obj, fov = "s2r1", cols = "polychrome", axes = TRUE)

and this was the session info:

R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] SeuratObject_5.0.1  Seurat_4.3.0.9002   sf_1.0-16           progressr_0.14.0    magrittr_2.0.3      BiocParallel_1.36.0
 [7] dplyr_1.1.4         hdf5r_1.3.10        data.table_1.15.4   ggplot2_3.5.0      

loaded via a namespace (and not attached):
  [1] DBI_1.2.2              deldir_2.0-4           pbapply_1.7-2          gridExtra_2.3          rlang_1.1.3           
  [6] RcppAnnoy_0.0.22       spatstat.geom_3.2-9    matrixStats_1.2.0      ggridges_0.5.6         e1071_1.7-14          
 [11] compiler_4.3.3         png_0.1-8              vctrs_0.6.5            reshape2_1.4.4         stringr_1.5.1         
 [16] pkgconfig_2.0.3        fastmap_1.1.1          labeling_0.4.3         utf8_1.2.4             promises_1.2.1        
 [21] tzdb_0.4.0             purrr_1.0.2            bit_4.0.5              jsonlite_1.8.8         goftest_1.2-3         
 [26] later_1.3.2            spatstat.utils_3.0-4   irlba_2.3.5.1          parallel_4.3.3         cluster_2.1.6         
 [31] R6_2.5.1               ica_1.0-3              spatstat.data_3.0-4    stringi_1.8.3          RColorBrewer_1.1-3    
 [36] reticulate_1.35.0      parallelly_1.37.1      lmtest_0.9-40          scattermore_1.2        assertthat_0.2.1      
 [41] Rcpp_1.0.12            tensor_1.5             future.apply_1.11.2    zoo_1.8-12             sctransform_0.4.1     
 [46] httpuv_1.6.15          Matrix_1.6-5           splines_4.3.3          igraph_2.0.3           tidyselect_1.2.1      
 [51] abind_1.4-5            rstudioapi_0.16.0      spatstat.random_3.2-3  spatstat.explore_3.2-7 codetools_0.2-19      
 [56] miniUI_0.1.1.1         listenv_0.9.1          lattice_0.22-5         tibble_3.2.1           plyr_1.8.9            
 [61] shiny_1.8.1.1          withr_3.0.0            ROCR_1.0-11            Rtsne_0.17             future_1.33.2         
 [66] survival_3.5-8         polyclip_1.10-6        units_0.8-5            proxy_0.4-27           fitdistrplus_1.1-11   
 [71] pillar_1.9.0           KernSmooth_2.23-22     plotly_4.10.4          generics_0.1.3         sp_2.1-3              
 [76] munsell_0.5.1          scales_1.3.0           globals_0.16.3         xtable_1.8-4           class_7.3-22          
 [81] glue_1.7.0             lazyeval_0.2.2         tools_4.3.3            RANN_2.6.1             leiden_0.4.3.1        
 [86] dotCall64_1.1-1        cowplot_1.1.3          grid_4.3.3             sfarrow_0.4.1          tidyr_1.3.1           
 [91] tidyverse_2.0.0        colorspace_2.1-0       nlme_3.1-164           patchwork_1.2.0        cli_3.6.2             
 [96] spatstat.sparse_3.0-3  spam_2.10-0            fansi_1.0.6            viridisLite_0.4.2      arrow_15.0.1          
[101] uwot_0.1.16            gtable_0.3.4           digest_0.6.35          classInt_0.4-10        ggrepel_0.9.5         
[106] farver_2.1.1           htmlwidgets_1.6.4      htmltools_0.5.8.1      lifecycle_1.0.4        httr_1.4.7            
[111] mime_0.12              bit64_4.0.5            MASS_7.3-60.0.1

@alikhuseynov
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you have these versions SeuratObject_5.0.1 Seurat_4.3.0.9002

  • This branch is for Seurat and SeuratObject v4 remotes::install_github(repo = 'alikhuseynov/seurat', ref = 'feat/vizgen')
  • This one is for v5 remotes::install_github(repo = 'alikhuseynov/seurat', ref = 'vizgen_seurat5') try to use this one.
    Also, HDF5 files are no longer the output from Vizgen, it's all in .parquet now.

could you show the complete output of messages (not a screenshot) when you run:

vizgen.obj <- LoadVizgen(data.dir = "C:/Users/gangliagurdian/Documents/practice/mouse_brain_vizgen_data", 
                        fov = "s2r1", 
                        use.BiocParallel = TRUE,
                        verbose = TRUE)

workers.MulticoreParam is not needed since you are on windows machine

check FOVs:

vizgen.obj[[Images(vizgen.obj)[1]]]
vizgen.obj[[Images(vizgen.obj)[1]]][["segmentation"]]
vizgen.obj[[Images(vizgen.obj)[1]]][["centroids"]] %>% str

show the object and plot of a given gene:

vizgen.obj
ImageFeaturePlot(vizgen.obj, features = "gene_name")

@angie-john
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This is the full output after running

vizgen.obj <- LoadVizgen(data.dir = "C:/Users/gangliagurdian/Documents/practice/mouse_brain_vizgen_data", 
                        fov = "s2r1", 
                        use.BiocParallel = TRUE,
                        verbose = TRUE) 

Warning in FUN(...) : Cannot find HDF5 file for field of view 270
Warning in FUN(...) : Cannot find HDF5 file for field of view 271
Warning in FUN(...) : Cannot find HDF5 file for field of view 272
Warning in FUN(...) : Cannot find HDF5 file for field of view 273
Warning in FUN(...) : Cannot find HDF5 file for field of view 274
Warning in FUN(...) : Cannot find HDF5 file for field of view 275
Warning in FUN(...) : Cannot find HDF5 file for field of view 276
Warning in FUN(...) : Cannot find HDF5 file for field of view 277
  |=======================                                                                                                    |  18%Warning in FUN(...) : Cannot find HDF5 file for field of view 278
Warning in FUN(...) : Cannot find HDF5 file for field of view 279
  |=======================                                                                                                    |  19%Warning in FUN(...) : Cannot find HDF5 file for field of view 280
Warning in FUN(...) : Cannot find HDF5 file for field of view 281
Warning in FUN(...) : Cannot find HDF5 file for field of view 282
Warning in FUN(...) : Cannot find HDF5 file for field of view 283
Warning in FUN(...) : Cannot find HDF5 file for field of view 284
Warning in FUN(...) : Cannot find HDF5 file for field of view 285
Warning in FUN(...) : Cannot find HDF5 file for field of view 286
Warning in FUN(...) : Cannot find HDF5 file for field of view 287
  |========================                                                                                                   |  19%Warning in FUN(...) : Cannot find HDF5 file for field of view 288
Warning in FUN(...) : Cannot find HDF5 file for field of view 289
Warning in FUN(...) : Cannot find HDF5 file for field of view 290
Warning in FUN(...) : Cannot find HDF5 file for field of view 291
Warning in FUN(...) : Cannot find HDF5 file for field of view 292
  |========================                                                                                                   |  20%Warning in FUN(...) : Cannot find HDF5 file for field of view 293
Warning in FUN(...) : Cannot find HDF5 file for field of view 294
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Warning in FUN(...) : Cannot find HDF5 file for field of view 297
  |=========================                                                                                                  |  20%Warning in FUN(...) : Cannot find HDF5 file for field of view 298
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  |=========================                                                                                                  |  21%Warning in FUN(...) : Cannot find HDF5 file for field of view 305
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  |==========================                                                                                                 |  21%Warning in FUN(...) : Cannot find HDF5 file for field of view 311
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  |===========================                                                                                                |  22%Warning in FUN(...) : Cannot find HDF5 file for field of view 321
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  |============================                                                                                               |  22%Warning in FUN(...) : Cannot find HDF5 file for field of view 331
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  |=============================                                                                                              |  23%Warning in FUN(...) : Cannot find HDF5 file for field of view 341
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  |=============================                                                                                              |  24%Warning in FUN(...) : Cannot find HDF5 file for field of view 345
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  |==============================                                                                                             |  25%Warning in FUN(...) : Cannot find HDF5 file for field of view 358
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  |===============================                                                                                            |  25%Warning in FUN(...) : Cannot find HDF5 file for field of view 361
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  |===============================                                                                                            |  26%Warning in FUN(...) : Cannot find HDF5 file for field of view 372
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  |=================================                                                                                          |  26%Warning in FUN(...) : Cannot find HDF5 file for field of view 384
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  |==================================                                                                                         |  27%Warning in FUN(...) : Cannot find HDF5 file for field of view 394
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  |==================================                                                                                         |  28%Warning in FUN(...) : Cannot find HDF5 file for field of view 397
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  |===================================                                                                                        |  28%Warning in FUN(...) : Cannot find HDF5 file for field of view 406
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  |===================================                                                                                        |  29%Warning in FUN(...) : Cannot find HDF5 file for field of view 411
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  |======================================                                                                                     |  31%Warning in FUN(...) : Cannot find HDF5 file for field of view 440
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  |=======================================                                                                                    |  31%Warning in FUN(...) : Cannot find HDF5 file for field of view 450
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  |=======================================                                                                                    |  32%Warning in FUN(...) : Cannot find HDF5 file for field of view 453
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  |=========================================                                                                                  |  34%Warning in FUN(...) : Cannot find HDF5 file for field of view 478
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  |==========================================                                                                                 |  34%Warning in FUN(...) : Cannot find HDF5 file for field of view 481
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Warning in FUN(...) : Cannot find HDF5 file for field of view 500
  |============================================                                                                               |  35%Warning in FUN(...) : Cannot find HDF5 file for field of view 501
  |============================================                                                                               |  36%Warning in FUN(...) : Cannot find HDF5 file for field of view 502
Warning in FUN(...) : Cannot find HDF5 file for field of view 507
Warning in FUN(...) : Cannot find HDF5 file for field of view 508
Warning in FUN(...) : Cannot find HDF5 file for field of view 509
Warning in FUN(...) : Cannot find HDF5 file for field of view 510
Warning in FUN(...) : Cannot find HDF5 file for field of view 511
Warning in FUN(...) : Cannot find HDF5 file for field of view 512
Warning in FUN(...) : Cannot find HDF5 file for field of view 513
Warning in FUN(...) : Cannot find HDF5 file for field of view 514
  |=============================================                                                                              |  36%Warning in FUN(...) : Cannot find HDF5 file for field of view 515
Warning in FUN(...) : Cannot find HDF5 file for field of view 516
Warning in FUN(...) : Cannot find HDF5 file for field of view 517
Warning in FUN(...) : Cannot find HDF5 file for field of view 518
  |=============================================                                                                              |  37%Warning in FUN(...) : Cannot find HDF5 file for field of view 519
Warning in FUN(...) : Cannot find HDF5 file for field of view 520
Warning in FUN(...) : Cannot find HDF5 file for field of view 521
Warning in FUN(...) : Cannot find HDF5 file for field of view 522
Warning in FUN(...) : Cannot find HDF5 file for field of view 523
Warning in FUN(...) : Cannot find HDF5 file for field of view 524
  |==============================================                                                                             |  37%Warning in FUN(...) : Cannot find HDF5 file for field of view 525
Warning in FUN(...) : Cannot find HDF5 file for field of view 526
Warning in FUN(...) : Cannot find HDF5 file for field of view 527
Warning in FUN(...) : Cannot find HDF5 file for field of view 528
Warning in FUN(...) : Cannot find HDF5 file for field of view 529
Warning in FUN(...) : Cannot find HDF5 file for field of view 530
  |==============================================                                                                             |  38%Warning in FUN(...) : Cannot find HDF5 file for field of view 531
Warning in FUN(...) : Cannot find HDF5 file for field of view 532
Warning in FUN(...) : Cannot find HDF5 file for field of view 533
Warning in FUN(...) : Cannot find HDF5 file for field of view 534
  |===============================================                                                                            |  38%Warning in FUN(...) : Cannot find HDF5 file for field of view 535
Warning in FUN(...) : Cannot find HDF5 file for field of view 536
Warning in FUN(...) : Cannot find HDF5 file for field of view 537
Warning in FUN(...) : Cannot find HDF5 file for field of view 538
Warning in FUN(...) : Cannot find HDF5 file for field of view 539
Warning in FUN(...) : Cannot find HDF5 file for field of view 540
Warning in FUN(...) : Cannot find HDF5 file for field of view 541
Warning in FUN(...) : Cannot find HDF5 file for field of view 542
Warning in FUN(...) : Cannot find HDF5 file for field of view 543
  |===============================================                                                                            |  39%Warning in FUN(...) : Cannot find HDF5 file for field of view 544
  |================================================                                                                           |  39%Warning in FUN(...) : Cannot find HDF5 file for field of view 545
Warning in FUN(...) : Cannot find HDF5 file for field of view 546
Warning in FUN(...) : Cannot find HDF5 file for field of view 547
Warning in FUN(...) : Cannot find HDF5 file for field of view 548
Warning in FUN(...) : Cannot find HDF5 file for field of view 549
Warning in FUN(...) : Cannot find HDF5 file for field of view 550
Warning in FUN(...) : Cannot find HDF5 file for field of view 551
Warning in FUN(...) : Cannot find HDF5 file for field of view 552
Warning in FUN(...) : Cannot find HDF5 file for field of view 553
Warning in FUN(...) : Cannot find HDF5 file for field of view 554
  |=================================================                                                                          |  39%Warning in FUN(...) : Cannot find HDF5 file for field of view 555
  |=================================================                                                                          |  40%Warning in FUN(...) : Cannot find HDF5 file for field of view 556
Warning in FUN(...) : Cannot find HDF5 file for field of view 557
Warning in FUN(...) : Cannot find HDF5 file for field of view 558
Warning in FUN(...) : Cannot find HDF5 file for field of view 559
Warning in FUN(...) : Cannot find HDF5 file for field of view 560
Warning in FUN(...) : Cannot find HDF5 file for field of view 561
Warning in FUN(...) : Cannot find HDF5 file for field of view 562
Warning in FUN(...) : Cannot find HDF5 file for field of view 563
Warning in FUN(...) : Cannot find HDF5 file for field of view 564
  |==================================================                                                                         |  40%Warning in FUN(...) : Cannot find HDF5 file for field of view 565
Warning in FUN(...) : Cannot find HDF5 file for field of view 566
Warning in FUN(...) : Cannot find HDF5 file for field of view 567
Warning in FUN(...) : Cannot find HDF5 file for field of view 568
  |==================================================                                                                         |  41%Warning in FUN(...) : Cannot find HDF5 file for field of view 569
Warning in FUN(...) : Cannot find HDF5 file for field of view 570
Warning in FUN(...) : Cannot find HDF5 file for field of view 571
Warning in FUN(...) : Cannot find HDF5 file for field of view 572
Warning in FUN(...) : Cannot find HDF5 file for field of view 577
Warning in FUN(...) : Cannot find HDF5 file for field of view 578
  |===================================================                                                                        |  41%Warning in FUN(...) : Cannot find HDF5 file for field of view 579
Warning in FUN(...) : Cannot find HDF5 file for field of view 580
Warning in FUN(...) : Cannot find HDF5 file for field of view 581
Warning in FUN(...) : Cannot find HDF5 file for field of view 582
Warning in FUN(...) : Cannot find HDF5 file for field of view 583
Warning in FUN(...) : Cannot find HDF5 file for field of view 584
  |===================================================                                                                        |  42%Warning in FUN(...) : Cannot find HDF5 file for field of view 585
Warning in FUN(...) : Cannot find HDF5 file for field of view 586
Warning in FUN(...) : Cannot find HDF5 file for field of view 587
Warning in FUN(...) : Cannot find HDF5 file for field of view 588
Warning in FUN(...) : Cannot find HDF5 file for field of view 589
  |====================================================                                                                       |  42%Warning in FUN(...) : Cannot find HDF5 file for field of view 590
Warning in FUN(...) : Cannot find HDF5 file for field of view 591
Warning in FUN(...) : Cannot find HDF5 file for field of view 592
Warning in FUN(...) : Cannot find HDF5 file for field of view 593
Warning in FUN(...) : Cannot find HDF5 file for field of view 594
Warning in FUN(...) : Cannot find HDF5 file for field of view 595
Warning in FUN(...) : Cannot find HDF5 file for field of view 596
  |====================================================                                                                       |  43%Warning in FUN(...) : Cannot find HDF5 file for field of view 597
Warning in FUN(...) : Cannot find HDF5 file for field of view 598
Warning in FUN(...) : Cannot find HDF5 file for field of view 599
  |=====================================================                                                                      |  43%Warning in FUN(...) : Cannot find HDF5 file for field of view 600
Warning in FUN(...) : Cannot find HDF5 file for field of view 601
Warning in FUN(...) : Cannot find HDF5 file for field of view 602
Warning in FUN(...) : Cannot find HDF5 file for field of view 603
Warning in FUN(...) : Cannot find HDF5 file for field of view 604
Warning in FUN(...) : Cannot find HDF5 file for field of view 605
Warning in FUN(...) : Cannot find HDF5 file for field of view 606
Warning in FUN(...) : Cannot find HDF5 file for field of view 607
Warning in FUN(...) : Cannot find HDF5 file for field of view 608
Warning in FUN(...) : Cannot find HDF5 file for field of view 609
  |======================================================                                                                     |  44%Warning in FUN(...) : Cannot find HDF5 file for field of view 610
Warning in FUN(...) : Cannot find HDF5 file for field of view 611
Warning in FUN(...) : Cannot find HDF5 file for field of view 612
Warning in FUN(...) : Cannot find HDF5 file for field of view 613
Warning in FUN(...) : Cannot find HDF5 file for field of view 614
Warning in FUN(...) : Cannot find HDF5 file for field of view 615
Warning in FUN(...) : Cannot find HDF5 file for field of view 616
Warning in FUN(...) : Cannot find HDF5 file for field of view 617
Warning in FUN(...) : Cannot find HDF5 file for field of view 618
Warning in FUN(...) : Cannot find HDF5 file for field of view 619
  |=======================================================                                                                    |  44%Warning in FUN(...) : Cannot find HDF5 file for field of view 620
Warning in FUN(...) : Cannot find HDF5 file for field of view 621
  |=======================================================                                                                    |  45%Warning in FUN(...) : Cannot find HDF5 file for field of view 622
Warning in FUN(...) : Cannot find HDF5 file for field of view 623
Warning in FUN(...) : Cannot find HDF5 file for field of view 624
Warning in FUN(...) : Cannot find HDF5 file for field of view 625
Warning in FUN(...) : Cannot find HDF5 file for field of view 626
Warning in FUN(...) : Cannot find HDF5 file for field of view 627
Warning in FUN(...) : Cannot find HDF5 file for field of view 628
Warning in FUN(...) : Cannot find HDF5 file for field of view 629
  |========================================================                                                                   |  45%Warning in FUN(...) : Cannot find HDF5 file for field of view 630
Warning in FUN(...) : Cannot find HDF5 file for field of view 631
Warning in FUN(...) : Cannot find HDF5 file for field of view 632
Warning in FUN(...) : Cannot find HDF5 file for field of view 633
Warning in FUN(...) : Cannot find HDF5 file for field of view 634
  |========================================================                                                                   |  46%Warning in FUN(...) : Cannot find HDF5 file for field of view 635
Warning in FUN(...) : Cannot find HDF5 file for field of view 636
Warning in FUN(...) : Cannot find HDF5 file for field of view 637
Warning in FUN(...) : Cannot find HDF5 file for field of view 638
Warning in FUN(...) : Cannot find HDF5 file for field of view 639
  |=========================================================                                                                  |  46%Warning in FUN(...) : Cannot find HDF5 file for field of view 640
Warning in FUN(...) : Cannot find HDF5 file for field of view 641
Warning in FUN(...) : Cannot find HDF5 file for field of view 642
Warning in FUN(...) : Cannot find HDF5 file for field of view 647
Warning in FUN(...) : Cannot find HDF5 file for field of view 648
Warning in FUN(...) : Cannot find HDF5 file for field of view 649
Warning in FUN(...) : Cannot find HDF5 file for field of view 650
  |=========================================================                                                                  |  47%Warning in FUN(...) : Cannot find HDF5 file for field of view 651
Warning in FUN(...) : Cannot find HDF5 file for field of view 652
Warning in FUN(...) : Cannot find HDF5 file for field of view 653
  |==========================================================                                                                 |  47%Warning in FUN(...) : Cannot find HDF5 file for field of view 654
Warning in FUN(...) : Cannot find HDF5 file for field of view 655
Warning in FUN(...) : Cannot find HDF5 file for field of view 656
Warning in FUN(...) : Cannot find HDF5 file for field of view 657
Warning in FUN(...) : Cannot find HDF5 file for field of view 658
Warning in FUN(...) : Cannot find HDF5 file for field of view 659
Warning in FUN(...) : Cannot find HDF5 file for field of view 660
Warning in FUN(...) : Cannot find HDF5 file for field of view 661
Warning in FUN(...) : Cannot find HDF5 file for field of view 662
  |==========================================================                                                                 |  48%Warning in FUN(...) : Cannot find HDF5 file for field of view 663
  |===========================================================                                                                |  48%Warning in FUN(...) : Cannot find HDF5 file for field of view 664
Warning in FUN(...) : Cannot find HDF5 file for field of view 665
Warning in FUN(...) : Cannot find HDF5 file for field of view 666
Warning in FUN(...) : Cannot find HDF5 file for field of view 667
Warning in FUN(...) : Cannot find HDF5 file for field of view 668
Warning in FUN(...) : Cannot find HDF5 file for field of view 669
Warning in FUN(...) : Cannot find HDF5 file for field of view 670
Warning in FUN(...) : Cannot find HDF5 file for field of view 671
Warning in FUN(...) : Cannot find HDF5 file for field of view 672
Warning in FUN(...) : Cannot find HDF5 file for field of view 673
  |============================================================                                                               |  48%Warning in FUN(...) : Cannot find HDF5 file for field of view 674
Warning in FUN(...) : Cannot find HDF5 file for field of view 675
  |============================================================                                                               |  49%Warning in FUN(...) : Cannot find HDF5 file for field of view 676
Warning in FUN(...) : Cannot find HDF5 file for field of view 677
Warning in FUN(...) : Cannot find HDF5 file for field of view 678
Warning in FUN(...) : Cannot find HDF5 file for field of view 679
Warning in FUN(...) : Cannot find HDF5 file for field of view 680
Warning in FUN(...) : Cannot find HDF5 file for field of view 681
Warning in FUN(...) : Cannot find HDF5 file for field of view 682
Warning in FUN(...) : Cannot find HDF5 file for field of view 683
  |=============================================================                                                              |  49%Warning in FUN(...) : Cannot find HDF5 file for field of view 684
Warning in FUN(...) : Cannot find HDF5 file for field of view 685
Warning in FUN(...) : Cannot find HDF5 file for field of view 686
Warning in FUN(...) : Cannot find HDF5 file for field of view 687
  |=============================================================                                                              |  50%Warning in FUN(...) : Cannot find HDF5 file for field of view 688
Warning in FUN(...) : Cannot find HDF5 file for field of view 689
Warning in FUN(...) : Cannot find HDF5 file for field of view 690
Warning in FUN(...) : Cannot find HDF5 file for field of view 691
Warning in FUN(...) : Cannot find HDF5 file for field of view 692
Warning in FUN(...) : Cannot find HDF5 file for field of view 693
  |==============================================================                                                             |  50%Warning in FUN(...) : Cannot find HDF5 file for field of view 694
Warning in FUN(...) : Cannot find HDF5 file for field of view 695
Warning in FUN(...) : Cannot find HDF5 file for field of view 696
Warning in FUN(...) : Cannot find HDF5 file for field of view 697
Warning in FUN(...) : Cannot find HDF5 file for field of view 698
Warning in FUN(...) : Cannot find HDF5 file for field of view 699
Warning in FUN(...) : Cannot find HDF5 file for field of view 700
  |==============================================================                                                             |  51%Warning in FUN(...) : Cannot find HDF5 file for field of view 701
Warning in FUN(...) : Cannot find HDF5 file for field of view 702
Warning in FUN(...) : Cannot find HDF5 file for field of view 703
Warning in FUN(...) : Cannot find HDF5 file for field of view 704
  |===============================================================                                                            |  51%Warning in FUN(...) : Cannot find HDF5 file for field of view 705
Warning in FUN(...) : Cannot find HDF5 file for field of view 706
Warning in FUN(...) : Cannot find HDF5 file for field of view 707
Warning in FUN(...) : Cannot find HDF5 file for field of view 708
Warning in FUN(...) : Cannot find HDF5 file for field of view 709
Warning in FUN(...) : Cannot find HDF5 file for field of view 710
Warning in FUN(...) : Cannot find HDF5 file for field of view 711
Warning in FUN(...) : Cannot find HDF5 file for field of view 712
  |===============================================================                                                            |  52%Warning in FUN(...) : Cannot find HDF5 file for field of view 716
Warning in FUN(...) : Cannot find HDF5 file for field of view 717
  |================================================================                                                           |  52%Warning in FUN(...) : Cannot find HDF5 file for field of view 718
Warning in FUN(...) : Cannot find HDF5 file for field of view 719
Warning in FUN(...) : Cannot find HDF5 file for field of view 720
Warning in FUN(...) : Cannot find HDF5 file for field of view 721
Warning in FUN(...) : Cannot find HDF5 file for field of view 722
Warning in FUN(...) : Cannot find HDF5 file for field of view 723
Warning in FUN(...) : Cannot find HDF5 file for field of view 724
Warning in FUN(...) : Cannot find HDF5 file for field of view 725
Warning in FUN(...) : Cannot find HDF5 file for field of view 726
Warning in FUN(...) : Cannot find HDF5 file for field of view 727
  |=================================================================                                                          |  52%Warning in FUN(...) : Cannot find HDF5 file for field of view 728
  |=================================================================                                                          |  53%Warning in FUN(...) : Cannot find HDF5 file for field of view 729
Warning in FUN(...) : Cannot find HDF5 file for field of view 730
Warning in FUN(...) : Cannot find HDF5 file for field of view 731
Warning in FUN(...) : Cannot find HDF5 file for field of view 732
Warning in FUN(...) : Cannot find HDF5 file for field of view 733
Warning in FUN(...) : Cannot find HDF5 file for field of view 734
Warning in FUN(...) : Cannot find HDF5 file for field of view 735
Warning in FUN(...) : Cannot find HDF5 file for field of view 736
Warning in FUN(...) : Cannot find HDF5 file for field of view 737
  |==================================================================                                                         |  53%Warning in FUN(...) : Cannot find HDF5 file for field of view 738
Warning in FUN(...) : Cannot find HDF5 file for field of view 739
Warning in FUN(...) : Cannot find HDF5 file for field of view 740
  |==================================================================                                                         |  54%Warning in FUN(...) : Cannot find HDF5 file for field of view 741
Warning in FUN(...) : Cannot find HDF5 file for field of view 742
Warning in FUN(...) : Cannot find HDF5 file for field of view 743
Warning in FUN(...) : Cannot find HDF5 file for field of view 744
Warning in FUN(...) : Cannot find HDF5 file for field of view 745
Warning in FUN(...) : Cannot find HDF5 file for field of view 746
Warning in FUN(...) : Cannot find HDF5 file for field of view 747
  |===================================================================                                                        |  54%Warning in FUN(...) : Cannot find HDF5 file for field of view 748
Warning in FUN(...) : Cannot find HDF5 file for field of view 749
Warning in FUN(...) : Cannot find HDF5 file for field of view 750
Warning in FUN(...) : Cannot find HDF5 file for field of view 751
Warning in FUN(...) : Cannot find HDF5 file for field of view 752
  |===================================================================                                                        |  55%Warning in FUN(...) : Cannot find HDF5 file for field of view 753
Warning in FUN(...) : Cannot find HDF5 file for field of view 754
Warning in FUN(...) : Cannot find HDF5 file for field of view 755
Warning in FUN(...) : Cannot find HDF5 file for field of view 756
Warning in FUN(...) : Cannot find HDF5 file for field of view 757
  |====================================================================                                                       |  55%Warning in FUN(...) : Cannot find HDF5 file for field of view 758
Warning in FUN(...) : Cannot find HDF5 file for field of view 759
Warning in FUN(...) : Cannot find HDF5 file for field of view 760
Warning in FUN(...) : Cannot find HDF5 file for field of view 761
Warning in FUN(...) : Cannot find HDF5 file for field of view 762
Warning in FUN(...) : Cannot find HDF5 file for field of view 763
Warning in FUN(...) : Cannot find HDF5 file for field of view 764
Warning in FUN(...) : Cannot find HDF5 file for field of view 765
  |====================================================================                                                       |  56%Warning in FUN(...) : Cannot find HDF5 file for field of view 766
Warning in FUN(...) : Cannot find HDF5 file for field of view 767
  |=====================================================================                                                      |  56%Warning in FUN(...) : Cannot find HDF5 file for field of view 768
Warning in FUN(...) : Cannot find HDF5 file for field of view 769
Warning in FUN(...) : Cannot find HDF5 file for field of view 770
Warning in FUN(...) : Cannot find HDF5 file for field of view 771
Warning in FUN(...) : Cannot find HDF5 file for field of view 772
Warning in FUN(...) : Cannot find HDF5 file for field of view 773
Warning in FUN(...) : Cannot find HDF5 file for field of view 774
Warning in FUN(...) : Cannot find HDF5 file for field of view 775
Warning in FUN(...) : Cannot find HDF5 file for field of view 776
Warning in FUN(...) : Cannot find HDF5 file for field of view 777
  |======================================================================                                                     |  57%Warning in FUN(...) : Cannot find HDF5 file for field of view 778
Warning in FUN(...) : Cannot find HDF5 file for field of view 779
Warning in FUN(...) : Cannot find HDF5 file for field of view 780
Warning in FUN(...) : Cannot find HDF5 file for field of view 781
Warning in FUN(...) : Cannot find HDF5 file for field of view 785
Warning in FUN(...) : Cannot find HDF5 file for field of view 786
Warning in FUN(...) : Cannot find HDF5 file for field of view 787
Warning in FUN(...) : Cannot find HDF5 file for field of view 788
Warning in FUN(...) : Cannot find HDF5 file for field of view 789
Warning in FUN(...) : Cannot find HDF5 file for field of view 790
  |=======================================================================                                                    |  57%Warning in FUN(...) : Cannot find HDF5 file for field of view 791
Warning in FUN(...) : Cannot find HDF5 file for field of view 792
Warning in FUN(...) : Cannot find HDF5 file for field of view 793
  |=======================================================================                                                    |  58%Warning in FUN(...) : Cannot find HDF5 file for field of view 794
Warning in FUN(...) : Cannot find HDF5 file for field of view 795
Warning in FUN(...) : Cannot find HDF5 file for field of view 796
Warning in FUN(...) : Cannot find HDF5 file for field of view 797
Warning in FUN(...) : Cannot find HDF5 file for field of view 798
Warning in FUN(...) : Cannot find HDF5 file for field of view 799
Warning in FUN(...) : Cannot find HDF5 file for field of view 800
  |========================================================================                                                   |  58%Warning in FUN(...) : Cannot find HDF5 file for field of view 801
Warning in FUN(...) : Cannot find HDF5 file for field of view 802
Warning in FUN(...) : Cannot find HDF5 file for field of view 803
Warning in FUN(...) : Cannot find HDF5 file for field of view 804
Warning in FUN(...) : Cannot find HDF5 file for field of view 805
  |========================================================================                                                   |  59%Warning in FUN(...) : Cannot find HDF5 file for field of view 806
Warning in FUN(...) : Cannot find HDF5 file for field of view 807
Warning in FUN(...) : Cannot find HDF5 file for field of view 808
Warning in FUN(...) : Cannot find HDF5 file for field of view 809
Warning in FUN(...) : Cannot find HDF5 file for field of view 810
Warning in FUN(...) : Cannot find HDF5 file for field of view 811
  |=========================================================================                                                  |  59%Warning in FUN(...) : Cannot find HDF5 file for field of view 812
Warning in FUN(...) : Cannot find HDF5 file for field of view 813
Warning in FUN(...) : Cannot find HDF5 file for field of view 814
Warning in FUN(...) : Cannot find HDF5 file for field of view 815
Warning in FUN(...) : Cannot find HDF5 file for field of view 816
Warning in FUN(...) : Cannot find HDF5 file for field of view 819
  |=========================================================================                                                  |  60%Warning in FUN(...) : Cannot find HDF5 file for field of view 820
Warning in FUN(...) : Cannot find HDF5 file for field of view 821
Warning in FUN(...) : Cannot find HDF5 file for field of view 822
Warning in FUN(...) : Cannot find HDF5 file for field of view 823
  |==========================================================================                                                 |  60%Warning in FUN(...) : Cannot find HDF5 file for field of view 824
Warning in FUN(...) : Cannot find HDF5 file for field of view 825
Warning in FUN(...) : Cannot find HDF5 file for field of view 826
Warning in FUN(...) : Cannot find HDF5 file for field of view 827
Warning in FUN(...) : Cannot find HDF5 file for field of view 828
Warning in FUN(...) : Cannot find HDF5 file for field of view 829
Warning in FUN(...) : Cannot find HDF5 file for field of view 830
Warning in FUN(...) : Cannot find HDF5 file for field of view 831
Warning in FUN(...) : Cannot find HDF5 file for field of view 832
  |==========================================================================                                                 |  61%Warning in FUN(...) : Cannot find HDF5 file for field of view 833
  |===========================================================================                                                |  61%Warning in FUN(...) : Cannot find HDF5 file for field of view 834
Warning in FUN(...) : Cannot find HDF5 file for field of view 835
Warning in FUN(...) : Cannot find HDF5 file for field of view 836
Warning in FUN(...) : Cannot find HDF5 file for field of view 837
Warning in FUN(...) : Cannot find HDF5 file for field of view 838
Warning in FUN(...) : Cannot find HDF5 file for field of view 839
Warning in FUN(...) : Cannot find HDF5 file for field of view 840
Warning in FUN(...) : Cannot find HDF5 file for field of view 841
Warning in FUN(...) : Cannot find HDF5 file for field of view 842
Warning in FUN(...) : Cannot find HDF5 file for field of view 843
  |============================================================================                                               |  61%Warning in FUN(...) : Cannot find HDF5 file for field of view 844
  |============================================================================                                               |  62%Warning in FUN(...) : Cannot find HDF5 file for field of view 845
Warning in FUN(...) : Cannot find HDF5 file for field of view 846
Warning in FUN(...) : Cannot find HDF5 file for field of view 847
Warning in FUN(...) : Cannot find HDF5 file for field of view 848
Warning in FUN(...) : Cannot find HDF5 file for field of view 849
Warning in FUN(...) : Cannot find HDF5 file for field of view 850
Warning in FUN(...) : Cannot find HDF5 file for field of view 855
Warning in FUN(...) : Cannot find HDF5 file for field of view 856
Warning in FUN(...) : Cannot find HDF5 file for field of view 857
  |=============================================================================                                              |  62%Warning in FUN(...) : Cannot find HDF5 file for field of view 858
Warning in FUN(...) : Cannot find HDF5 file for field of view 859
Warning in FUN(...) : Cannot find HDF5 file for field of view 860
Warning in FUN(...) : Cannot find HDF5 file for field of view 861
  |=============================================================================                                              |  63%Warning in FUN(...) : Cannot find HDF5 file for field of view 862
Warning in FUN(...) : Cannot find HDF5 file for field of view 863
Warning in FUN(...) : Cannot find HDF5 file for field of view 864
Warning in FUN(...) : Cannot find HDF5 file for field of view 865
Warning in FUN(...) : Cannot find HDF5 file for field of view 866
Warning in FUN(...) : Cannot find HDF5 file for field of view 867
  |==============================================================================                                             |  63%Warning in FUN(...) : Cannot find HDF5 file for field of view 868
Warning in FUN(...) : Cannot find HDF5 file for field of view 869
Warning in FUN(...) : Cannot find HDF5 file for field of view 870
Warning in FUN(...) : Cannot find HDF5 file for field of view 871
Warning in FUN(...) : Cannot find HDF5 file for field of view 872
Warning in FUN(...) : Cannot find HDF5 file for field of view 873
  |==============================================================================                                             |  64%Warning in FUN(...) : Cannot find HDF5 file for field of view 874
Warning in FUN(...) : Cannot find HDF5 file for field of view 875
Warning in FUN(...) : Cannot find HDF5 file for field of view 876
Warning in FUN(...) : Cannot find HDF5 file for field of view 877
  |===============================================================================                                            |  64%Warning in FUN(...) : Cannot find HDF5 file for field of view 878
Warning in FUN(...) : Cannot find HDF5 file for field of view 879
Warning in FUN(...) : Cannot find HDF5 file for field of view 880
Warning in FUN(...) : Cannot find HDF5 file for field of view 881
Warning in FUN(...) : Cannot find HDF5 file for field of view 882
Warning in FUN(...) : Cannot find HDF5 file for field of view 883
Warning in FUN(...) : Cannot find HDF5 file for field of view 884
Warning in FUN(...) : Cannot find HDF5 file for field of view 885
Warning in FUN(...) : Cannot find HDF5 file for field of view 886
  |===============================================================================                                            |  65%Warning in FUN(...) : Cannot find HDF5 file for field of view 887
  |================================================================================                                           |  65%Warning in FUN(...) : Cannot find HDF5 file for field of view 888
Warning in FUN(...) : Cannot find HDF5 file for field of view 889
Warning in FUN(...) : Cannot find HDF5 file for field of view 890
Warning in FUN(...) : Cannot find HDF5 file for field of view 891
Warning in FUN(...) : Cannot find HDF5 file for field of view 892
Warning in FUN(...) : Cannot find HDF5 file for field of view 893
Warning in FUN(...) : Cannot find HDF5 file for field of view 894
Warning in FUN(...) : Cannot find HDF5 file for field of view 895
Warning in FUN(...) : Cannot find HDF5 file for field of view 896
Warning in FUN(...) : Cannot find HDF5 file for field of view 897
  |=================================================================================                                          |  65%Warning in FUN(...) : Cannot find HDF5 file for field of view 898
  |=================================================================================                                          |  66%Warning in FUN(...) : Cannot find HDF5 file for field of view 899
Warning in FUN(...) : Cannot find HDF5 file for field of view 900
Warning in FUN(...) : Cannot find HDF5 file for field of view 901
Warning in FUN(...) : Cannot find HDF5 file for field of view 902
Warning in FUN(...) : Cannot find HDF5 file for field of view 903
Warning in FUN(...) : Cannot find HDF5 file for field of view 904
Warning in FUN(...) : Cannot find HDF5 file for field of view 905
Warning in FUN(...) : Cannot find HDF5 file for field of view 906
Warning in FUN(...) : Cannot find HDF5 file for field of view 907
  |==================================================================================                                         |  66%Warning in FUN(...) : Cannot find HDF5 file for field of view 908
Warning in FUN(...) : Cannot find HDF5 file for field of view 909
Warning in FUN(...) : Cannot find HDF5 file for field of view 910
  |==================================================================================                                         |  67%Warning in FUN(...) : Cannot find HDF5 file for field of view 911
Warning in FUN(...) : Cannot find HDF5 file for field of view 912
Warning in FUN(...) : Cannot find HDF5 file for field of view 913
Warning in FUN(...) : Cannot find HDF5 file for field of view 914
Warning in FUN(...) : Cannot find HDF5 file for field of view 915
Warning in FUN(...) : Cannot find HDF5 file for field of view 916
Warning in FUN(...) : Cannot find HDF5 file for field of view 917
Warning in FUN(...) : Cannot find HDF5 file for field of view 918
  |===================================================================================                                        |  67%Warning in FUN(...) : Cannot find HDF5 file for field of view 919
Warning in FUN(...) : Cannot find HDF5 file for field of view 920
Warning in FUN(...) : Cannot find HDF5 file for field of view 921
Warning in FUN(...) : Cannot find HDF5 file for field of view 922
Warning in FUN(...) : Cannot find HDF5 file for field of view 926
  |===================================================================================                                        |  68%Warning in FUN(...) : Cannot find HDF5 file for field of view 927
Warning in FUN(...) : Cannot find HDF5 file for field of view 928
Warning in FUN(...) : Cannot find HDF5 file for field of view 929
Warning in FUN(...) : Cannot find HDF5 file for field of view 930
Warning in FUN(...) : Cannot find HDF5 file for field of view 931
  |====================================================================================                                       |  68%Warning in FUN(...) : Cannot find HDF5 file for field of view 932
Warning in FUN(...) : Cannot find HDF5 file for field of view 933
Warning in FUN(...) : Cannot find HDF5 file for field of view 934
Warning in FUN(...) : Cannot find HDF5 file for field of view 935
Warning in FUN(...) : Cannot find HDF5 file for field of view 936
Warning in FUN(...) : Cannot find HDF5 file for field of view 937
Warning in FUN(...) : Cannot find HDF5 file for field of view 938
  |====================================================================================                                       |  69%Warning in FUN(...) : Cannot find HDF5 file for field of view 939
Warning in FUN(...) : Cannot find HDF5 file for field of view 940
Warning in FUN(...) : Cannot find HDF5 file for field of view 941
  |=====================================================================================                                      |  69%Warning in FUN(...) : Cannot find HDF5 file for field of view 942
Warning in FUN(...) : Cannot find HDF5 file for field of view 943
Warning in FUN(...) : Cannot find HDF5 file for field of view 944
Warning in FUN(...) : Cannot find HDF5 file for field of view 945
Warning in FUN(...) : Cannot find HDF5 file for field of view 946
Warning in FUN(...) : Cannot find HDF5 file for field of view 947
Warning in FUN(...) : Cannot find HDF5 file for field of view 948
Warning in FUN(...) : Cannot find HDF5 file for field of view 949
Warning in FUN(...) : Cannot find HDF5 file for field of view 950
Warning in FUN(...) : Cannot find HDF5 file for field of view 951
  |======================================================================================                                     |  70%Warning in FUN(...) : Cannot find HDF5 file for field of view 952
Warning in FUN(...) : Cannot find HDF5 file for field of view 953
Warning in FUN(...) : Cannot find HDF5 file for field of view 954
Warning in FUN(...) : Cannot find HDF5 file for field of view 955
Warning in FUN(...) : Cannot find HDF5 file for field of view 956
Warning in FUN(...) : Cannot find HDF5 file for field of view 957
Warning in FUN(...) : Cannot find HDF5 file for field of view 958
Warning in FUN(...) : Cannot find HDF5 file for field of view 959
Warning in FUN(...) : Cannot find HDF5 file for field of view 960
Warning in FUN(...) : Cannot find HDF5 file for field of view 961
  |=======================================================================================                                    |  70%Warning in FUN(...) : Cannot find HDF5 file for field of view 962
Warning in FUN(...) : Cannot find HDF5 file for field of view 963
  |=======================================================================================                                    |  71%Warning in FUN(...) : Cannot find HDF5 file for field of view 964
Warning in FUN(...) : Cannot find HDF5 file for field of view 965
Warning in FUN(...) : Cannot find HDF5 file for field of view 966
Warning in FUN(...) : Cannot find HDF5 file for field of view 967
Warning in FUN(...) : Cannot find HDF5 file for field of view 968
Warning in FUN(...) : Cannot find HDF5 file for field of view 969
Warning in FUN(...) : Cannot find HDF5 file for field of view 970
Warning in FUN(...) : Cannot find HDF5 file for field of view 971
  |========================================================================================                                   |  71%Warning in FUN(...) : Cannot find HDF5 file for field of view 972
Warning in FUN(...) : Cannot find HDF5 file for field of view 973
Warning in FUN(...) : Cannot find HDF5 file for field of view 974
Warning in FUN(...) : Cannot find HDF5 file for field of view 975
Warning in FUN(...) : Cannot find HDF5 file for field of view 976
  |========================================================================================                                   |  72%Warning in FUN(...) : Cannot find HDF5 file for field of view 977
Warning in FUN(...) : Cannot find HDF5 file for field of view 978
Warning in FUN(...) : Cannot find HDF5 file for field of view 979
Warning in FUN(...) : Cannot find HDF5 file for field of view 980
Warning in FUN(...) : Cannot find HDF5 file for field of view 981
  |=========================================================================================                                  |  72%Warning in FUN(...) : Cannot find HDF5 file for field of view 982
Warning in FUN(...) : Cannot find HDF5 file for field of view 983
Warning in FUN(...) : Cannot find HDF5 file for field of view 984
Warning in FUN(...) : Cannot find HDF5 file for field of view 985
Warning in FUN(...) : Cannot find HDF5 file for field of view 986
Warning in FUN(...) : Cannot find HDF5 file for field of view 987
Warning in FUN(...) : Cannot find HDF5 file for field of view 988
  |=========================================================================================                                  |  73%Warning in FUN(...) : Cannot find HDF5 file for field of view 989
Warning in FUN(...) : Cannot find HDF5 file for field of view 990
Warning in FUN(...) : Cannot find HDF5 file for field of view 991
  |==========================================================================================                                 |  73%Warning in FUN(...) : Cannot find HDF5 file for field of view 994
Warning in FUN(...) : Cannot find HDF5 file for field of view 995
Warning in FUN(...) : Cannot find HDF5 file for field of view 996
Warning in FUN(...) : Cannot find HDF5 file for field of view 997
Warning in FUN(...) : Cannot find HDF5 file for field of view 998
Warning in FUN(...) : Cannot find HDF5 file for field of view 999
  |===============================================================================================                            |  77%Warning in FUN(...) : Cannot find HDF5 file for field of view 1045
Warning in FUN(...) : Cannot find HDF5 file for field of view 1046
Warning in FUN(...) : Cannot find HDF5 file for field of view 1047
Warning in FUN(...) : Cannot find HDF5 file for field of view 1048
Warning in FUN(...) : Cannot find HDF5 file for field of view 1049
Warning in FUN(...) : Cannot find HDF5 file for field of view 1050
Warning in FUN(...) : Cannot find HDF5 file for field of view 1051
Warning in FUN(...) : Cannot find HDF5 file for field of view 1052
  |===============================================================================================                            |  78%Warning in FUN(...) : Cannot find HDF5 file for field of view 1053
Warning in FUN(...) : Cannot find HDF5 file for field of view 1054
  |================================================================================================                           |  78%Warning in FUN(...) : Cannot find HDF5 file for field of view 1055
Warning in FUN(...) : Cannot find HDF5 file for field of view 1056
Warning in FUN(...) : Cannot find HDF5 file for field of view 1057
Warning in FUN(...) : Cannot find HDF5 file for field of view 1058
Warning in FUN(...) : Cannot find HDF5 file for field of view 1063
Warning in FUN(...) : Cannot find HDF5 file for field of view 1064
Warning in FUN(...) : Cannot find HDF5 file for field of view 1065
Warning in FUN(...) : Cannot find HDF5 file for field of view 1066
Warning in FUN(...) : Cannot find HDF5 file for field of view 1067
Warning in FUN(...) : Cannot find HDF5 file for field of view 1068
  |=================================================================================================                          |  79%Warning in FUN(...) : Cannot find HDF5 file for field of view 1069
Warning in FUN(...) : Cannot find HDF5 file for field of view 1070
Warning in FUN(...) : Cannot find HDF5 file for field of view 1071
Warning in FUN(...) : Cannot find HDF5 file for field of view 1072
Warning in FUN(...) : Cannot find HDF5 file for field of view 1073
Warning in FUN(...) : Cannot find HDF5 file for field of view 1074
Warning in FUN(...) : Cannot find HDF5 file for field of view 1075
Warning in FUN(...) : Cannot find HDF5 file for field of view 1076
Warning in FUN(...) : Cannot find HDF5 file for field of view 1077
Warning in FUN(...) : Cannot find HDF5 file for field of view 1078
  |==================================================================================================                         |  79%Warning in FUN(...) : Cannot find HDF5 file for field of view 1079
Warning in FUN(...) : Cannot find HDF5 file for field of view 1080
Warning in FUN(...) : Cannot find HDF5 file for field of view 1081
  |==================================================================================================                         |  80%Warning in FUN(...) : Cannot find HDF5 file for field of view 1082
Warning in FUN(...) : Cannot find HDF5 file for field of view 1083
Warning in FUN(...) : Cannot find HDF5 file for field of view 1084
Warning in FUN(...) : Cannot find HDF5 file for field of view 1085
Warning in FUN(...) : Cannot find HDF5 file for field of view 1086
Warning in FUN(...) : Cannot find HDF5 file for field of view 1087
Warning in FUN(...) : Cannot find HDF5 file for field of view 1088
  |===================================================================================================                        |  80%Warning in FUN(...) : Cannot find HDF5 file for field of view 1089
Warning in FUN(...) : Cannot find HDF5 file for field of view 1090
Warning in FUN(...) : Cannot find HDF5 file for field of view 1091
Warning in FUN(...) : Cannot find HDF5 file for field of view 1092
Warning in FUN(...) : Cannot find HDF5 file for field of view 1093
  |===================================================================================================                        |  81%Warning in FUN(...) : Cannot find HDF5 file for field of view 1094
Warning in FUN(...) : Cannot find HDF5 file for field of view 1095
Warning in FUN(...) : Cannot find HDF5 file for field of view 1096
Warning in FUN(...) : Cannot find HDF5 file for field of view 1097
Warning in FUN(...) : Cannot find HDF5 file for field of view 1098
  |====================================================================================================                       |  81%Warning in FUN(...) : Cannot find HDF5 file for field of view 1099
Warning in FUN(...) : Cannot find HDF5 file for field of view 1100
Warning in FUN(...) : Cannot find HDF5 file for field of view 1101
Warning in FUN(...) : Cannot find HDF5 file for field of view 1102
Warning in FUN(...) : Cannot find HDF5 file for field of view 1103
Warning in FUN(...) : Cannot find HDF5 file for field of view 1104
Warning in FUN(...) : Cannot find HDF5 file for field of view 1105
Warning in FUN(...) : Cannot find HDF5 file for field of view 1106
  |====================================================================================================                       |  82%Warning in FUN(...) : Cannot find HDF5 file for field of view 1107
Warning in FUN(...) : Cannot find HDF5 file for field of view 1108
  |=====================================================================================================                      |  82%Warning in FUN(...) : Cannot find HDF5 file for field of view 1109
Warning in FUN(...) : Cannot find HDF5 file for field of view 1110
Warning in FUN(...) : Cannot find HDF5 file for field of view 1111
Warning in FUN(...) : Cannot find HDF5 file for field of view 1112
Warning in FUN(...) : Cannot find HDF5 file for field of view 1113
Warning in FUN(...) : Cannot find HDF5 file for field of view 1114
Warning in FUN(...) : Cannot find HDF5 file for field of view 1115
Warning in FUN(...) : Cannot find HDF5 file for field of view 1116
Warning in FUN(...) : Cannot find HDF5 file for field of view 1117
Warning in FUN(...) : Cannot find HDF5 file for field of view 1118
  |======================================================================================================                     |  83%Warning in FUN(...) : Cannot find HDF5 file for field of view 1119
Warning in FUN(...) : Cannot find HDF5 file for field of view 1120
Warning in FUN(...) : Cannot find HDF5 file for field of view 1121
Warning in FUN(...) : Cannot find HDF5 file for field of view 1122
Warning in FUN(...) : Cannot find HDF5 file for field of view 1123
Warning in FUN(...) : Cannot find HDF5 file for field of view 1124
Warning in FUN(...) : Cannot find HDF5 file for field of view 1128
Warning in FUN(...) : Cannot find HDF5 file for field of view 1129
Warning in FUN(...) : Cannot find HDF5 file for field of view 1130
Warning in FUN(...) : Cannot find HDF5 file for field of view 1131
Warning in FUN(...) : Cannot find HDF5 file for field of view 1132
  |=======================================================================================================                    |  83%Warning in FUN(...) : Cannot find HDF5 file for field of view 1133
Warning in FUN(...) : Cannot find HDF5 file for field of view 1134
  |=======================================================================================================                    |  84%Warning in FUN(...) : Cannot find HDF5 file for field of view 1135
Warning in FUN(...) : Cannot find HDF5 file for field of view 1136
Warning in FUN(...) : Cannot find HDF5 file for field of view 1137
Warning in FUN(...) : Cannot find HDF5 file for field of view 1138
Warning in FUN(...) : Cannot find HDF5 file for field of view 1139
Warning in FUN(...) : Cannot find HDF5 file for field of view 1140
Warning in FUN(...) : Cannot find HDF5 file for field of view 1141
Warning in FUN(...) : Cannot find HDF5 file for field of view 1142
  |========================================================================================================                   |  84%Warning in FUN(...) : Cannot find HDF5 file for field of view 1143
Warning in FUN(...) : Cannot find HDF5 file for field of view 1144
Warning in FUN(...) : Cannot find HDF5 file for field of view 1145
Warning in FUN(...) : Cannot find HDF5 file for field of view 1146
  |========================================================================================================                   |  85%Warning in FUN(...) : Cannot find HDF5 file for field of view 1147
Warning in FUN(...) : Cannot find HDF5 file for field of view 1148
Warning in FUN(...) : Cannot find HDF5 file for field of view 1149
Warning in FUN(...) : Cannot find HDF5 file for field of view 1150
Warning in FUN(...) : Cannot find HDF5 file for field of view 1151
Warning in FUN(...) : Cannot find HDF5 file for field of view 1152
  |=========================================================================================================                  |  85%Warning in FUN(...) : Cannot find HDF5 file for field of view 1153
Warning in FUN(...) : Cannot find HDF5 file for field of view 1154
Warning in FUN(...) : Cannot find HDF5 file for field of view 1155
Warning in FUN(...) : Cannot find HDF5 file for field of view 1156
Warning in FUN(...) : Cannot find HDF5 file for field of view 1157
Warning in FUN(...) : Cannot find HDF5 file for field of view 1158
  |=========================================================================================================                  |  86%Warning in FUN(...) : Cannot find HDF5 file for field of view 1159
Warning in FUN(...) : Cannot find HDF5 file for field of view 1160
Warning in FUN(...) : Cannot find HDF5 file for field of view 1161
Warning in FUN(...) : Cannot find HDF5 file for field of view 1162
  |==========================================================================================================                 |  86%Warning in FUN(...) : Cannot find HDF5 file for field of view 1163
Warning in FUN(...) : Cannot find HDF5 file for field of view 1164
Warning in FUN(...) : Cannot find HDF5 file for field of view 1165
Warning in FUN(...) : Cannot find HDF5 file for field of view 1166
Warning in FUN(...) : Cannot find HDF5 file for field of view 1167
Warning in FUN(...) : Cannot find HDF5 file for field of view 1168
Warning in FUN(...) : Cannot find HDF5 file for field of view 1169
Warning in FUN(...) : Cannot find HDF5 file for field of view 1170
Warning in FUN(...) : Cannot find HDF5 file for field of view 1171
  |==========================================================================================================                 |  87%Warning in FUN(...) : Cannot find HDF5 file for field of view 1172
  |===========================================================================================================                |  87%Warning in FUN(...) : Cannot find HDF5 file for field of view 1173
Warning in FUN(...) : Cannot find HDF5 file for field of view 1174
Warning in FUN(...) : Cannot find HDF5 file for field of view 1175
Warning in FUN(...) : Cannot find HDF5 file for field of view 1176
Warning in FUN(...) : Cannot find HDF5 file for field of view 1177
Warning in FUN(...) : Cannot find HDF5 file for field of view 1178
Warning in FUN(...) : Cannot find HDF5 file for field of view 1179
Warning in FUN(...) : Cannot find HDF5 file for field of view 1180
Warning in FUN(...) : Cannot find HDF5 file for field of view 1181
Warning in FUN(...) : Cannot find HDF5 file for field of view 1182
  |============================================================================================================               |  87%Warning in FUN(...) : Cannot find HDF5 file for field of view 1183
  |============================================================================================================               |  88%Warning in FUN(...) : Cannot find HDF5 file for field of view 1184
Warning in FUN(...) : Cannot find HDF5 file for field of view 1185
Warning in FUN(...) : Cannot find HDF5 file for field of view 1186
Warning in FUN(...) : Cannot find HDF5 file for field of view 1187
Warning in FUN(...) : Cannot find HDF5 file for field of view 1191
Warning in FUN(...) : Cannot find HDF5 file for field of view 1192
Warning in FUN(...) : Cannot find HDF5 file for field of view 1193
Warning in FUN(...) : Cannot find HDF5 file for field of view 1194
Warning in FUN(...) : Cannot find HDF5 file for field of view 1195
  |=============================================================================================================              |  88%Warning in FUN(...) : Cannot find HDF5 file for field of view 1196
Warning in FUN(...) : Cannot find HDF5 file for field of view 1197
Warning in FUN(...) : Cannot find HDF5 file for field of view 1198
Warning in FUN(...) : Cannot find HDF5 file for field of view 1199
  |=============================================================================================================              |  89%Warning in FUN(...) : Cannot find HDF5 file for field of view 1200
Warning in FUN(...) : Cannot find HDF5 file for field of view 1201
Warning in FUN(...) : Cannot find HDF5 file for field of view 1202
Warning in FUN(...) : Cannot find HDF5 file for field of view 1203
Warning in FUN(...) : Cannot find HDF5 file for field of view 1204
Warning in FUN(...) : Cannot find HDF5 file for field of view 1205
  |==============================================================================================================             |  89%Warning in FUN(...) : Cannot find HDF5 file for field of view 1206
Warning in FUN(...) : Cannot find HDF5 file for field of view 1207
Warning in FUN(...) : Cannot find HDF5 file for field of view 1208
Warning in FUN(...) : Cannot find HDF5 file for field of view 1209
Warning in FUN(...) : Cannot find HDF5 file for field of view 1210
Warning in FUN(...) : Cannot find HDF5 file for field of view 1211
  |==============================================================================================================             |  90%Warning in FUN(...) : Cannot find HDF5 file for field of view 1212
Warning in FUN(...) : Cannot find HDF5 file for field of view 1213
Warning in FUN(...) : Cannot find HDF5 file for field of view 1214
Warning in FUN(...) : Cannot find HDF5 file for field of view 1215
  |===============================================================================================================            |  90%Warning in FUN(...) : Cannot find HDF5 file for field of view 1216
Warning in FUN(...) : Cannot find HDF5 file for field of view 1217
Warning in FUN(...) : Cannot find HDF5 file for field of view 1218
Warning in FUN(...) : Cannot find HDF5 file for field of view 1220
Warning in FUN(...) : Cannot find HDF5 file for field of view 1221
Warning in FUN(...) : Cannot find HDF5 file for field of view 1222
Warning in FUN(...) : Cannot find HDF5 file for field of view 1223
Warning in FUN(...) : Cannot find HDF5 file for field of view 1224
Warning in FUN(...) : Cannot find HDF5 file for field of view 1225
  |===============================================================================================================            |  91%Warning in FUN(...) : Cannot find HDF5 file for field of view 1226
  |================================================================================================================           |  91%Warning in FUN(...) : Cannot find HDF5 file for field of view 1227
Warning in FUN(...) : Cannot find HDF5 file for field of view 1228
Warning in FUN(...) : Cannot find HDF5 file for field of view 1229
Warning in FUN(...) : Cannot find HDF5 file for field of view 1230
Warning in FUN(...) : Cannot find HDF5 file for field of view 1231
Warning in FUN(...) : Cannot find HDF5 file for field of view 1232
Warning in FUN(...) : Cannot find HDF5 file for field of view 1233
Warning in FUN(...) : Cannot find HDF5 file for field of view 1234
Warning in FUN(...) : Cannot find HDF5 file for field of view 1235
Warning in FUN(...) : Cannot find HDF5 file for field of view 1236
  |=================================================================================================================          |  91%Warning in FUN(...) : Cannot find HDF5 file for field of view 1237
  |=================================================================================================================          |  92%Warning in FUN(...) : Cannot find HDF5 file for field of view 1238
Warning in FUN(...) : Cannot find HDF5 file for field of view 1239
Warning in FUN(...) : Cannot find HDF5 file for field of view 1240
Warning in FUN(...) : Cannot find HDF5 file for field of view 1241
Warning in FUN(...) : Cannot find HDF5 file for field of view 1242
Warning in FUN(...) : Cannot find HDF5 file for field of view 1243
Warning in FUN(...) : Cannot find HDF5 file for field of view 1244
Warning in FUN(...) : Cannot find HDF5 file for field of view 1245
Warning in FUN(...) : Cannot find HDF5 file for field of view 1250
Warning in FUN(...) : Cannot find HDF5 file for field of view 1251
  |==================================================================================================================         |  92%Warning in FUN(...) : Cannot find HDF5 file for field of view 1252
Warning in FUN(...) : Cannot find HDF5 file for field of view 1253
  |==================================================================================================================         |  93%Warning in FUN(...) : Cannot find HDF5 file for field of view 1254
Warning in FUN(...) : Cannot find HDF5 file for field of view 1255
Warning in FUN(...) : Cannot find HDF5 file for field of view 1256
Warning in FUN(...) : Cannot find HDF5 file for field of view 1257
Warning in FUN(...) : Cannot find HDF5 file for field of view 1258
Warning in FUN(...) : Cannot find HDF5 file for field of view 1259
Warning in FUN(...) : Cannot find HDF5 file for field of view 1260
Warning in FUN(...) : Cannot find HDF5 file for field of view 1261
  |===================================================================================================================        |  93%Warning in FUN(...) : Cannot find HDF5 file for field of view 1262
Warning in FUN(...) : Cannot find HDF5 file for field of view 1263
Warning in FUN(...) : Cannot find HDF5 file for field of view 1264
Warning in FUN(...) : Cannot find HDF5 file for field of view 1265
Warning in FUN(...) : Cannot find HDF5 file for field of view 1266
  |===================================================================================================================        |  94%Warning in FUN(...) : Cannot find HDF5 file for field of view 1267
Warning in FUN(...) : Cannot find HDF5 file for field of view 1268
Warning in FUN(...) : Cannot find HDF5 file for field of view 1269
Warning in FUN(...) : Cannot find HDF5 file for field of view 1270
Warning in FUN(...) : Cannot find HDF5 file for field of view 1271
  |====================================================================================================================       |  94%Warning in FUN(...) : Cannot find HDF5 file for field of view 1272
Warning in FUN(...) : Cannot find HDF5 file for field of view 1275
Warning in FUN(...) : Cannot find HDF5 file for field of view 1276
Warning in FUN(...) : Cannot find HDF5 file for field of view 1277
Warning in FUN(...) : Cannot find HDF5 file for field of view 1278
Warning in FUN(...) : Cannot find HDF5 file for field of view 1279
Warning in FUN(...) : Cannot find HDF5 file for field of view 1280
  |====================================================================================================================       |  95%Warning in FUN(...) : Cannot find HDF5 file for field of view 1281
Warning in FUN(...) : Cannot find HDF5 file for field of view 1282
Warning in FUN(...) : Cannot find HDF5 file for field of view 1283
  |=====================================================================================================================      |  95%Warning in FUN(...) : Cannot find HDF5 file for field of view 1284
Warning in FUN(...) : Cannot find HDF5 file for field of view 1285
Warning in FUN(...) : Cannot find HDF5 file for field of view 1286
Warning in FUN(...) : Cannot find HDF5 file for field of view 1287
Warning in FUN(...) : Cannot find HDF5 file for field of view 1288
Warning in FUN(...) : Cannot find HDF5 file for field of view 1289
Warning in FUN(...) : Cannot find HDF5 file for field of view 1290
Warning in FUN(...) : Cannot find HDF5 file for field of view 1291
Warning in FUN(...) : Cannot find HDF5 file for field of view 1292
Warning in FUN(...) : Cannot find HDF5 file for field of view 1293
  |======================================================================================================================     |  96%Warning in FUN(...) : Cannot find HDF5 file for field of view 1294
Warning in FUN(...) : Cannot find HDF5 file for field of view 1295
Warning in FUN(...) : Cannot find HDF5 file for field of view 1296
Warning in FUN(...) : Cannot find HDF5 file for field of view 1302
Warning in FUN(...) : Cannot find HDF5 file for field of view 1303
Warning in FUN(...) : Cannot find HDF5 file for field of view 1304
Warning in FUN(...) : Cannot find HDF5 file for field of view 1305
Warning in FUN(...) : Cannot find HDF5 file for field of view 1306
Warning in FUN(...) : Cannot find HDF5 file for field of view 1307
Warning in FUN(...) : Cannot find HDF5 file for field of view 1308
  |=======================================================================================================================    |  96%Warning in FUN(...) : Cannot find HDF5 file for field of view 1309
Warning in FUN(...) : Cannot find HDF5 file for field of view 1310
  |=======================================================================================================================    |  97%Warning in FUN(...) : Cannot find HDF5 file for field of view 1311
Warning in FUN(...) : Cannot find HDF5 file for field of view 1312
Warning in FUN(...) : Cannot find HDF5 file for field of view 1313
Warning in FUN(...) : Cannot find HDF5 file for field of view 1314
Warning in FUN(...) : Cannot find HDF5 file for field of view 1315
Warning in FUN(...) : Cannot find HDF5 file for field of view 1316
Warning in FUN(...) : Cannot find HDF5 file for field of view 1317
Warning in FUN(...) : Cannot find HDF5 file for field of view 1318
  |========================================================================================================================   |  97%Warning in FUN(...) : Cannot find HDF5 file for field of view 1319
Warning in FUN(...) : Cannot find HDF5 file for field of view 1320
Warning in FUN(...) : Cannot find HDF5 file for field of view 1322
Warning in FUN(...) : Cannot find HDF5 file for field of view 1323
  |========================================================================================================================   |  98%Warning in FUN(...) : Cannot find HDF5 file for field of view 1324
Warning in FUN(...) : Cannot find HDF5 file for field of view 1325
Warning in FUN(...) : Cannot find HDF5 file for field of view 1326
Warning in FUN(...) : Cannot find HDF5 file for field of view 1327
Warning in FUN(...) : Cannot find HDF5 file for field of view 1328
Warning in FUN(...) : Cannot find HDF5 file for field of view 1329
  |=========================================================================================================================  |  98%Warning in FUN(...) : Cannot find HDF5 file for field of view 1330
Warning in FUN(...) : Cannot find HDF5 file for field of view 1331
Warning in FUN(...) : Cannot find HDF5 file for field of view 1332
Warning in FUN(...) : Cannot find HDF5 file for field of view 1333
Warning in FUN(...) : Cannot find HDF5 file for field of view 1334
Warning in FUN(...) : Cannot find HDF5 file for field of view 1335
Warning in FUN(...) : Cannot find HDF5 file for field of view 1336
  |=========================================================================================================================  |  99%Warning in FUN(...) : Cannot find HDF5 file for field of view 1337
Warning in FUN(...) : Cannot find HDF5 file for field of view 1344
Warning in FUN(...) : Cannot find HDF5 file for field of view 1345
  |========================================================================================================================== |  99%Warning in FUN(...) : Cannot find HDF5 file for field of view 1346
Warning in FUN(...) : Cannot find HDF5 file for field of view 1347
Warning in FUN(...) : Cannot find HDF5 file for field of view 1348
Warning in FUN(...) : Cannot find HDF5 file for field of view 1349
Warning in FUN(...) : Cannot find HDF5 file for field of view 1350
Warning in FUN(...) : Cannot find HDF5 file for field of view 1351
Warning in FUN(...) : Cannot find HDF5 file for field of view 1352
Warning in FUN(...) : Cannot find HDF5 file for field of view 1353
Warning in FUN(...) : Cannot find HDF5 file for field of view 1354
  |========================================================================================================================== | 100%Warning in FUN(...) : Cannot find HDF5 file for field of view 1355
  |===========================================================================================================================| 100%Warning in FUN(...) : Cannot find HDF5 file for field of view 1359
Warning in FUN(...) : Cannot find HDF5 file for field of view 1360
Warning in FUN(...) : Cannot find HDF5 file for field of view 1361
Warning in FUN(...) : Cannot find HDF5 file for field of view 1362
Warning in FUN(...) : Cannot find HDF5 file for field of view 1363


Warning in ReadVizgen(data.dir = data.dir, mol.type = mol.type, filter = filter,  :
  80223 cells missing polygon information
Creating Seurat object..
Creating FOVs..

>>> using segmentations
>>> adding metadata infos
>>> adding FOV
>>> all counts are > 0
Updating object:
Validating object structure
Updating object slots
Ensuring keys are in the proper structure
Ensuring keys are in the proper structure
Ensuring feature names don't have underscores or pipes
Updating slots in Vizgen
Updating slots in s2r1
Validating object structure for Assay ‘Vizgen’
Validating object structure for FOV ‘s2r1’
Object representation is consistent with the most current Seurat version
Object is ready!

This is the output after checking FOVs:

> vizgen.obj[[Images(vizgen.obj)[1]]]
Spatial coordinates for 3323 cells and 483 molecules
 First 10 molecules: Abcc9, Ackr1, Ackr2, Ackr3, Ackr4, Acte1
Default segmentation boundary: centroids 
 1 other segmentation boundaries present: segmentation 
Associated assay: Vizgen 
Key: Vizgen_ 
> vizgen.obj[[Images(vizgen.obj)[1]]][["segmentation"]]
A spatial segmentation for 3323 cells
> vizgen.obj[[Images(vizgen.obj)[1]]][["centroids"]] %>% str
Formal class 'Centroids' [package "SeuratObject"] with 7 slots
  ..@ cells      : chr [1:3323] "102585870299473950909222347372414346703" "102639946463719293231619392056336745817" "105321502672874017012721239064937326417" "106343835140223509995966804116631126801" ...
  ..@ nsides     : int 0
  ..@ radius     : num 80
  ..@ theta      : num 0
  ..@ coords     : num [1:3323, 1:2] 1076 1055 1081 1051 1046 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : NULL
  .. .. ..$ : chr [1:2] "x" "y"
  ..@ bbox       : num [1:2, 1:2] 1010 1985 7096 7442
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "x" "y"
  .. .. ..$ : chr [1:2] "min" "max"
  ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slot
  .. .. ..@ projargs: chr NA

and this is the object and plot:

> vizgen.obj
An object of class Seurat 
966 features across 83546 samples within 2 assays 
Active assay: SCT (483 features, 483 variable features)
 3 layers present: counts, data, scale.data
 1 other assay present: Vizgen
 2 dimensional reductions calculated: pca, umap
 1 spatial field of view present: s2r1
> ImageFeaturePlot(vizgen.obj, features = "Slc17a7")
Warning: No FOV associated with assay 'SCT', using global default FOV

image

@alikhuseynov
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vizgen.obj[[Images(vizgen.obj)[1]]][["segmentation"]]
A spatial segmentation for 3323 cells

ok, it does read some segmentations

It seems to be an issue here ->
https://github.com/alikhuseynov/seurat/blob/vizgen_seurat5/R/preprocessing.R#L3100-L3101
or here -> https://github.com/satijalab/seurat/blob/master/R/preprocessing.R#L2778-L2780
basically sp$fov is kinda not recongnized.
I don't have a bandwidth to troubleshoot right now. If you only want to try out stuff with Vizgen data, I would suggest use another public dataset with .parquet files.

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@groverj3 @alikhuseynov @angie-john