From 4af2523307eb8e78c39857a3127b1f2ecb998328 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Thu, 6 Feb 2020 19:54:06 +0100
Subject: [PATCH] Remove obsoloete files
---
data/0.6.5/misc/dynamic_segmentations.json | 29 ++++++++++++++++++++++
data/images.json | 1 -
data/postprocess.json | 1 -
data/privates.json | 1 -
data/segmentations.json | 1 -
5 files changed, 29 insertions(+), 4 deletions(-)
create mode 100644 data/0.6.5/misc/dynamic_segmentations.json
delete mode 100644 data/images.json
delete mode 100644 data/postprocess.json
delete mode 100644 data/privates.json
delete mode 100644 data/segmentations.json
diff --git a/data/0.6.5/misc/dynamic_segmentations.json b/data/0.6.5/misc/dynamic_segmentations.json
new file mode 100644
index 0000000..bea02b5
--- /dev/null
+++ b/data/0.6.5/misc/dynamic_segmentations.json
@@ -0,0 +1,29 @@
+{
+ "sbem-6dpf-1-whole-segmented-cells": {
+ "PainteraProject:": [
+ "/g/kreshuk/data/arendt/platyneris_v1/data.n5",
+ "volumes/paintera/proofread_cells"
+ ],
+ "Postprocess": {
+ "BoundaryKey": "volumes/affinities/s1",
+ "BoundaryPath": "/g/kreshuk/data/arendt/platyneris_v1/data.n5",
+ "LabelSegmentation": false,
+ "MaxSegmentNumber": 32700
+ },
+ "TableUpdateFunction": "make_cell_tables"
+ },
+ "sbem-6dpf-1-whole-segmented-cilia": {
+ "PainteraProject:": [
+ "/g/kreshuk/data/arendt/platyneris_v1/data.n5",
+ "volumes/paintera/proofread_cilia"
+ ],
+ "TableUpdateFunction": "make_cilia_tables"
+ },
+ "sbem-6dpf-1-whole-segmented-nuclei": {
+ "PainteraProject:": [
+ "/g/kreshuk/data/arendt/platyneris_v1/data.n5",
+ "volumes/paintera/nuclei"
+ ],
+ "TableUpdateFunction": "make_nuclei_tables"
+ }
+}
\ No newline at end of file
diff --git a/data/images.json b/data/images.json
deleted file mode 100644
index 350bdc4..0000000
--- a/data/images.json
+++ /dev/null
@@ -1 +0,0 @@
-["sbem-6dpf-1-whole-raw", "sbem-6dpf-1-whole-mask-resin", "sbem-6dpf-1-whole-mask-inside", "sbem-6dpf-1-whole-mask-outside", "prospr-6dpf-1-whole-ENR69-BCA1-MED", "prospr-6dpf-1-whole-AllCR2-MED", "prospr-6dpf-1-whole-ANPRB-MED", "prospr-6dpf-1-whole-Calmodulin-MED", "prospr-6dpf-1-whole-ENR22-CO1A1-MED", "prospr-6dpf-1-whole-ENR39-RPC2-MED", "prospr-6dpf-1-whole-ChAT-MED", "prospr-6dpf-1-whole-Arx-MED", "prospr-6dpf-1-whole-Brn124-MED", "prospr-6dpf-1-whole-ANPRA-MED", "prospr-6dpf-1-whole-Beta3-MED", "prospr-6dpf-1-whole-DbhLike-MED", "prospr-6dpf-1-whole-Chx10-MED", "prospr-6dpf-1-whole-AP2-MED", "prospr-6dpf-1-whole-ENR20-PPIB-MED", "prospr-6dpf-1-whole-ENR62-NB5R3-MED", "prospr-6dpf-1-whole-COE-MED", "prospr-6dpf-1-whole-ENR57-Junctophilin1-MED", "prospr-6dpf-1-whole-ENR16-ODO2-MED", "prospr-6dpf-1-whole-ENR64-PSMF1-MED", "prospr-6dpf-1-whole-ENR6-Nucleolin-MED", "prospr-6dpf-1-whole-ENR34-MTHFSD-MED", "prospr-6dpf-1-whole-ENR54-Boule-like-MED", "prospr-6dpf-1-whole-ENR19-FboxLike-MED", "prospr-6dpf-1-whole-ENR4-SND1-MED", "prospr-6dpf-1-whole-ENR12-UNC22-MED", "prospr-6dpf-1-whole-Ash-MED", "prospr-6dpf-1-whole-ENR3-JKIP3-MED", "prospr-6dpf-1-whole-ENR13-NDUS1-MED", "prospr-6dpf-1-whole-ASCb-MED", "prospr-6dpf-1-whole-Bmpr1-MED", "prospr-6dpf-1-whole-AllCR1-MED", "prospr-6dpf-1-whole-ENR46-Calexcitin2-MED", "prospr-6dpf-1-whole-BarH1-MED", "prospr-6dpf-1-whole-BAIAP-MED", "prospr-6dpf-1-whole-ENR32-GRIK3-MED", "prospr-6dpf-1-whole-ENR25-Synaptopodin-MED", "prospr-6dpf-1-whole-ENR10-UPP-MED", "prospr-6dpf-1-whole-ENR1-PGAM-MED", "prospr-6dpf-1-whole-Cal2-MED", "prospr-6dpf-1-whole-Brn3a-MED", "prospr-6dpf-1-whole-DopaRD2-MED", "prospr-6dpf-1-whole-Dach-MED", "prospr-6dpf-1-whole-ENR2-RYR2-MED", "prospr-6dpf-1-whole-ENR29-USP9X-MED", "prospr-6dpf-1-whole-ENR30-CCG5-MED", "prospr-6dpf-1-whole-ENR31-Leucin-rich-MED", "prospr-6dpf-1-whole-AChE-MED", "prospr-6dpf-1-whole-ENR8-Non-muscle-MHC-MED", "prospr-6dpf-1-whole-ENR71-Patched-MED", "prospr-6dpf-1-whole-Edu42to48-MED", "prospr-6dpf-1-whole-FOR-MED", "prospr-6dpf-1-whole-ENR9-NOE1-MED", "prospr-6dpf-1-whole-GAD-MED", "prospr-6dpf-1-whole-ElaV-MED", "prospr-6dpf-1-whole-FVRI-MED", "prospr-6dpf-1-whole-FoxN4-MED", "prospr-6dpf-1-whole-FoxD3-MED", "prospr-6dpf-1-whole-GCB-MED", "prospr-6dpf-1-whole-GCD-MED", "prospr-6dpf-1-whole-GPCR2-MED", "prospr-6dpf-1-whole-GPCR32-MED", "prospr-6dpf-1-whole-GPCR209-MED", "prospr-6dpf-1-whole-GPCR203-MED", "prospr-6dpf-1-whole-Glt1-MED", "prospr-6dpf-1-whole-GnRH-MED", "prospr-6dpf-1-whole-GPCR210-MED", "prospr-6dpf-1-whole-GPPCR21-MED", "prospr-6dpf-1-whole-Gucy-MED", "prospr-6dpf-1-whole-GnrhR-MED", "prospr-6dpf-1-whole-Mitf-MED", "prospr-6dpf-1-whole-Hr38-MED", "prospr-6dpf-1-whole-Hb9-MED", "prospr-6dpf-1-whole-Hox7-MED", "prospr-6dpf-1-whole-Hox4-MED", "prospr-6dpf-1-whole-Loc28250-MED", "prospr-6dpf-1-whole-Loc5285ct-MED", "prospr-6dpf-1-whole-Lhx3-MED", "prospr-6dpf-1-whole-GlyT-MED", "prospr-6dpf-1-whole-Gata123-MED", "prospr-6dpf-1-whole-Lhx15-MED", "prospr-6dpf-1-whole-HCN1-MED", "prospr-6dpf-1-whole-Kv33e-MED", "prospr-6dpf-1-whole-MRLC2-MED", "prospr-6dpf-1-whole-Loc8913nt-MED", "prospr-6dpf-1-whole-Loc77859-MED", "prospr-6dpf-1-whole-NOV2-NOV2-MED", "prospr-6dpf-1-whole-Hand-MED", "prospr-6dpf-1-whole-Isl-MED", "prospr-6dpf-1-whole-HNF6-MED", "prospr-6dpf-1-whole-Lmo4-MED", "prospr-6dpf-1-whole-Kv33b-MED", "prospr-6dpf-1-whole-Grm7-MED", "prospr-6dpf-1-whole-NOV1-globin-like-MED", "prospr-6dpf-1-whole-Lmx1-MED", "prospr-6dpf-1-whole-Lhx2-MED", "prospr-6dpf-1-whole-NMDAR-MED", "prospr-6dpf-1-whole-Maf-MED", "prospr-6dpf-1-whole-NOV18-CEPU1-MED", "prospr-6dpf-1-whole-MHCL4-MED", "prospr-6dpf-1-whole-NOV29-NOV29-MED", "prospr-6dpf-1-whole-Munc22-MED", "prospr-6dpf-1-whole-NOV50-GDPD1-MED", "prospr-6dpf-1-whole-NPR1a-MED", "prospr-6dpf-1-whole-P56-MED", "prospr-6dpf-1-whole-NOV45-TMTC3-MED", "prospr-6dpf-1-whole-NOV52-KANL3-MED", "prospr-6dpf-1-whole-NOV15-OLM2A-MED", "prospr-6dpf-1-whole-Olig-MED", "prospr-6dpf-1-whole-PDF-MED", "prospr-6dpf-1-whole-Netrin-MED", "prospr-6dpf-1-whole-NOV6-Stathmin-MED", "prospr-6dpf-1-whole-NeuroD-MED", "prospr-6dpf-1-whole-Ngb-MED", "prospr-6dpf-1-whole-Pax258-MED", "prospr-6dpf-1-whole-Pde9-MED", "prospr-6dpf-1-whole-PLCg-MED", "prospr-6dpf-1-whole-Pax6-MED", "prospr-6dpf-1-whole-PCDH15-MED", "prospr-6dpf-1-whole-Pea3-MED", "prospr-6dpf-1-whole-Prdm8-MED", "prospr-6dpf-1-whole-Phc2-MED", "prospr-6dpf-1-whole-Pikachu-MED", "prospr-6dpf-1-whole-PitxB-MED", "prospr-6dpf-1-whole-Phox2b-MED", "prospr-6dpf-1-whole-RIMS-MED", "prospr-6dpf-1-whole-Ptf1-MED", "prospr-6dpf-1-whole-edu5to6at6dpf-MED", "prospr-6dpf-1-whole-edu4to5at6dpf-MED", "prospr-6dpf-1-whole-edu3to4at6dpf-MED", "prospr-6dpf-1-whole-Rab3-MED", "prospr-6dpf-1-whole-Robo-MED", "prospr-6dpf-1-whole-Sox4-MED", "prospr-6dpf-1-whole-Prox-MED", "prospr-6dpf-1-whole-Scn8aa-MED", "prospr-6dpf-1-whole-Syt7-MED", "prospr-6dpf-1-whole-Syt-MED", "prospr-6dpf-1-whole-Slit-MED", "prospr-6dpf-1-whole-Sim1-MED", "prospr-6dpf-1-whole-Sox2-MED", "prospr-6dpf-1-whole-SoxB12-MED", "prospr-6dpf-1-whole-TrpH-MED", "prospr-6dpf-1-whole-Sp8-MED", "prospr-6dpf-1-whole-SoxB2-MED", "prospr-6dpf-1-whole-Sema2-MED", "prospr-6dpf-1-whole-TrpV-MED", "prospr-6dpf-1-whole-Syta-MED", "prospr-6dpf-1-whole-Tbx20-MED", "prospr-6dpf-1-whole-TRPV4-MED", "prospr-6dpf-1-whole-TH-MED", "prospr-6dpf-1-whole-Syt12-MED", "prospr-6dpf-1-whole-Tbh-MED", "prospr-6dpf-1-whole-TIMP-MED", "prospr-6dpf-1-whole-VAChT-MED", "prospr-6dpf-1-whole-TRPV5-MED", "prospr-6dpf-1-whole-Wnt16-MED", "prospr-6dpf-1-whole-bsx-MED", "prospr-6dpf-1-whole-Tal-MED", "prospr-6dpf-1-whole-UNCS-MED", "prospr-6dpf-1-whole-ascII-MED", "prospr-6dpf-1-whole-Wnt5-MED", "prospr-6dpf-1-whole-VegfR-MED", "prospr-6dpf-1-whole-VGluT-MED", "prospr-6dpf-1-whole-delta-MED", "prospr-6dpf-1-whole-eve-MED", "prospr-6dpf-1-whole-cnga-MED", "prospr-6dpf-1-whole-asicalpha-MED", "prospr-6dpf-1-whole-eya-MED", "prospr-6dpf-1-whole-VAT1L-MED", "prospr-6dpf-1-whole-ascI-MED", "prospr-6dpf-1-whole-dbx1-MED", "prospr-6dpf-1-whole-Twist-MED", "prospr-6dpf-1-whole-gpb-MED", "prospr-6dpf-1-whole-dlx-MED", "prospr-6dpf-1-whole-lbx1b-MED", "prospr-6dpf-1-whole-catL-MED", "prospr-6dpf-1-whole-nk22-MED", "prospr-6dpf-1-whole-nAchR-MED", "prospr-6dpf-1-whole-irx2546-MED", "prospr-6dpf-1-whole-ato2-MED", "prospr-6dpf-1-whole-lhx6-MED", "prospr-6dpf-1-whole-fezf-MED", "prospr-6dpf-1-whole-hox1-MED", "prospr-6dpf-1-whole-gsx-MED", "prospr-6dpf-1-whole-irx6-MED", "prospr-6dpf-1-whole-ngn-MED", "prospr-6dpf-1-whole-tlx-MED", "prospr-6dpf-1-whole-nk21-MED", "prospr-6dpf-1-whole-mecom-MED", "prospr-6dpf-1-whole-muncB-MED", "prospr-6dpf-1-whole-trk-MED", "prospr-6dpf-1-whole-nk6-MED", "prospr-6dpf-1-whole-sert-MED", "prospr-6dpf-1-whole-nompc3-MED", "prospr-6dpf-1-whole-msx-MED", "prospr-6dpf-1-whole-paraxis-MED", "prospr-6dpf-1-whole-neog-MED", "prospr-6dpf-1-whole-otp-MED", "prospr-6dpf-1-whole-segmented-Glands", "prospr-6dpf-1-whole-rx-MED", "prospr-6dpf-1-whole-segmented-AllGlands", "prospr-6dpf-1-whole-pkd2-MED", "prospr-6dpf-1-whole-segmented-Head", "prospr-6dpf-1-whole-segmented-CrypticSegment", "prospr-6dpf-1-whole-pkd1-MED", "prospr-6dpf-1-whole-ntrps-MED", "prospr-6dpf-1-whole-uncx-MED", "prospr-6dpf-1-whole-six12-MED", "prospr-6dpf-1-whole-segmented-Pygidium", "prospr-6dpf-1-whole-six4-MED", "prospr-6dpf-1-whole-segmented-PNS", "prospr-6dpf-1-whole-segmented-RestOfAnimal", "prospr-6dpf-1-whole-segmented-Stomodeum", "prospr-6dpf-1-whole-segmented-VNC", "prospr-6dpf-1-whole-segmented-ProSPr6-Ref", "sbem-6dpf-1-whole-mask-extrapolated", "xray-6dpf-1-whole-raw"]
diff --git a/data/postprocess.json b/data/postprocess.json
deleted file mode 100644
index d83f671..0000000
--- a/data/postprocess.json
+++ /dev/null
@@ -1 +0,0 @@
-{"sbem-6dpf-1-whole-segmented-cells-labels": {"boundary_path": "/g/kreshuk/data/arendt/platyneris_v1/data.n5", "boundary_key": "volumes/affinities/s1", "max_segment_number": 32700, "label_segmentation": false}}
diff --git a/data/privates.json b/data/privates.json
deleted file mode 100644
index a3c4d14..0000000
--- a/data/privates.json
+++ /dev/null
@@ -1 +0,0 @@
-["sbem-6dpf-1-whole-traces-labels", "xray-6dpf-1-whole-raw"]
diff --git a/data/segmentations.json b/data/segmentations.json
deleted file mode 100644
index 4391a66..0000000
--- a/data/segmentations.json
+++ /dev/null
@@ -1 +0,0 @@
-{"sbem-6dpf-1-whole-segmented-chromatin-labels": {"is_static": true, "has_tables": true}, "sbem-6dpf-1-whole-segmented-tissue-labels": {"is_static": true, "has_tables": true}, "sbem-6dpf-1-whole-segmented-muscle": {"is_static": true, "has_tables": false}, "sbem-6dpf-1-whole-segmented-cells-labels": {"is_static": false, "paintera_project": ["/g/kreshuk/data/arendt/platyneris_v1/data.n5", "volumes/paintera/proofread_cells"], "resolution": [0.025, 0.02, 0.02], "table_update_function": "make_cell_tables"}, "sbem-6dpf-1-whole-segmented-nuclei-labels": {"is_static": false, "paintera_project": ["/g/kreshuk/data/arendt/platyneris_v1/data.n5", "volumes/paintera/nuclei"], "resolution": [0.1, 0.08, 0.08], "table_update_function": "make_nucleus_tables"}, "sbem-6dpf-1-whole-segmented-cilia-labels": {"is_static": false, "paintera_project": ["/g/kreshuk/data/arendt/platyneris_v1/data.n5", "volumes/paintera/cilia_label_multiset"], "resolution": [0.025, 0.01, 0.01], "table_update_function": "make_cilia_tables"}, "sbem-6dpf-1-whole-segmented-ariande-neuropil": {"is_static": true, "has_tables": false}, "sbem-6dpf-1-whole-segmented-cats-neuropil": {"is_static": true, "has_tables": false}, "sbem-6dpf-1-whole-traces-labels": {"is_static": true, "has_tables": true}, "prospr-6dpf-1-whole-virtual-cells-labels": {"is_static": true, "has_tables": true}, "sbem-6dpf-1-whole-segmented-ganglia-labels": {"is_static": true, "has_tables": true}, "sbem-6dpf-1-whole-segmented-midgut": {"is_static": true, "has_tables": false}}
--
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