nettracer3d 0.5.4__py3-none-any.whl → 0.5.5__py3-none-any.whl

{nettracer3d-0.5.4.dist-info → nettracer3d-0.5.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nettracer3d
-Version: 0.5.4
+Version: 0.5.5
 Summary: Scripts for intializing and analyzing networks from segmentations of three dimensional images.
 Author-email: Liam McLaughlin <mclaughlinliam99@gmail.com>
 Project-URL: User_Tutorial, https://www.youtube.com/watch?v=cRatn5VTWDY
@@ -44,10 +44,10 @@ NetTracer3D is free to use/fork for academic/nonprofit use so long as citation i
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 0.5.4 updates --
+-- Version 0.5.5 updates --
 
-1. Added new function to GUI in image -> overlays -> color nodes/edges. Generates a rgb array corresponding to the nodes/edge labels where each node/edge (depending which array is selected) is randomly assigned a unique rgb color in an overlay channel. This can be used, for example, to color code labeled branches for easy identification of which branch is which.
+1. When the highlight overlay is being used in big overlays (and therefore defaulting to the mini overlay), updated system to just make one 2d overlay that regenerates on slice movement. Decided this was better than having it sit in a bigger 3d array when said array wasn't being used for anything and had to be rebuilt on slice movement or 3d operations anyway.
 
-2. Improved highlight overlay general functionality (for selecting nodes/edges). Previously selecting a node/edge had the program attempting to create an equal sized array as an overlay, find all objects corresponding to the selected ones, fill those into the new highlight overlay, then overlay that image. This was understandably quite slow in big arrays where the system was wasting a lot of time searching the entire array every time something was selected. New version retains this functionality for arrays below 125 million voxels, since search time is rather manageable at that size. For larger arrays, it instead draws the highlight for the selected objects only into the current slice, rendering a new slice whenever the user scrolls in the stack (although the entire highlight overlay is still initialized as a placeholder). Functions that require the use of the entire highlight overlay (such as masking) are correspondingly updated to draw the entirety of the highlight overlay before executing (when the system has up until that point been drawing slices one at a time). This will likely be the retained behavior moving forward, although to eliminate this behavior, one can open nettracer_gui.py and set self.mini_thresh to some comically large value. The new highlight overlay seems to work effectively the same but faster in my testing although it is possible a bug slipped through, which I will fix if informed about (or if I find it myself).
+2. For the random forrest segmenter, added the option to segment by 2D slice instead of 3D. In short, the 3D version was very greedy with its RAM usage and essentially computes a set of feature maps for the target array that are equivalent dims. By default it makes 7 of these, so a 1 GB array is going to demand 7GB of RAM to store its feature maps. The 2D slice version segments by 2D slice instead, meaning it stores only feature maps for slices with actual slices on them for training the model, and then for predicting voxel foreground/background, it computes the feature maps for the current slice (admittedly in the threadpool so this is amplified by core amount in the CPU but generally speaking this will save a lot of RAM). The reason I made this segmenter is to give NetTracer3D all the bells and whistles to let a user do everything in one program, but admittedly there are more efficient ML segmenters out there, such as through FIJI's big data viewer which is a lot better at handling big arrays in memory. I considered a way to compute 3D feature maps one at a time, save them in chunks to hard mem, and then open them while doing the chunked total segmentation but frankly this would likely be too slow to want to use so I will just suggest using 2D slice segmenter if RAM runs low.
 
-3. For the machine learning segmenter, changed the system to attempt to segment the image by chunking the array into the largest possible chunks that can be divided across all CPU cores. Previously the system split the array into 64^3 voxel sized chunks and passed those to the CPU cores until everything was processed. I am not sure which version is more efficient/faster so this is somewhat of a test. In theory the new behavior could be faster because it asking Python to interpret less stuff. 
+I do not anticipate any major updates for this project for the foreseeable future beyond bug fixes. 

{nettracer3d-0.5.4.dist-info → nettracer3d-0.5.5.dist-info}/RECORD

@@ -4,18 +4,18 @@ nettracer3d/hub_getter.py,sha256=KiNtxdajLkwB1ftslvrh1FE1Ch9ZCFEmHSEEotwR-To,829
 nettracer3d/modularity.py,sha256=V1f3s_vGd8EuVz27mzq6ycIGr0BWIpH7c7NU4QjgAHU,30247
 nettracer3d/morphology.py,sha256=yQ0GuieMVXOQpaohZlPnkEXEuCUjf8Fg352axyK8nbM,10755
 nettracer3d/nettracer.py,sha256=OE95IH1TfAZvT-htv1LEhw1EpnnEpkA83R5EcGMQDQg,209828
-nettracer3d/nettracer_gui.py,sha256=fOKzicFOX9z-MEf_aD1SV8P4BuLKOdi6K1pxH-tiqrk,357091
+nettracer3d/nettracer_gui.py,sha256=lKNl6T9998fMIYKrWdOhoAQlOLGeCiSaAP2chXCIDdQ,365336
 nettracer3d/network_analysis.py,sha256=MJBBjslA1k_R8ymid77U-qGSgzxFVfzGVQhE0IdhnbE,48046
 nettracer3d/network_draw.py,sha256=F7fw6Pcf4qWOhdKwLmhwqWdschbDlHzwCVolQC9imeU,14117
 nettracer3d/node_draw.py,sha256=k3sCTfUCJs3aH1C1q1gTNxDz9EAQbBd1hsUIJajxRx8,9823
 nettracer3d/proximity.py,sha256=FnIiI_AzfXd22HwCIFIyQRZxKYJ8YscIDdPnIv-wsO4,10560
 nettracer3d/run.py,sha256=xYeaAc8FCx8MuzTGyL3NR3mK7WZzffAYAH23bNRZYO4,127
-nettracer3d/segmenter.py,sha256=5Dqo_q-m28cYq4ROBhc4lyWjJnYK7ETTiRXyU_QdVXU,29688
+nettracer3d/segmenter.py,sha256=hqe7VLRkil65d_KYyUwWbU7SbM7v-krVSeZfLUlHlfY,49587
 nettracer3d/simple_network.py,sha256=fP1gkDdtQcHruEZpUdasKdZeVacoLOxKhR3bY0L1CAQ,15426
 nettracer3d/smart_dilate.py,sha256=Kekm6YIVlJniMvJMG6_AwwNmCqK2l4Qtvg9VzzqPKMw,24600
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-nettracer3d-0.5.4.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
-nettracer3d-0.5.4.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
-nettracer3d-0.5.4.dist-info/RECORD,,
+nettracer3d-0.5.5.dist-info/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
+nettracer3d-0.5.5.dist-info/METADATA,sha256=8t96LyM9LOlvtwllVY0XrFszSZ5pj1J8t6wjPdVQ7Us,4746
+nettracer3d-0.5.5.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
+nettracer3d-0.5.5.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
+nettracer3d-0.5.5.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
+nettracer3d-0.5.5.dist-info/RECORD,,

{nettracer3d-0.5.4.dist-info → nettracer3d-0.5.5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (75.8.2)
 Root-Is-Purelib: true
 Tag: py3-none-any