nettracer3d 0.5.3__py3-none-any.whl → 0.5.5__py3-none-any.whl

{nettracer3d-0.5.3.dist-info → nettracer3d-0.5.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nettracer3d
-Version: 0.5.3
+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
@@ -44,9 +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 0.5.3 updates --
+-- Version 0.5.5 updates --
 
-1. Improved calculate volumes method. Previous method used np.argwhere() to count voxels of labeled objects in parallel which was quite strenuous in large arrays with many objects. New method uses np.bincount() which uses optimized numpy C libraries to do the same.
-2. scipy.ndimage.find_objects() method was replaced as the method to find bounding boxes for objects when searching for object neighborhoods for the morphological proximity network and the edge < > node interaction quantification. This new version should be substantially faster in big arrays with many labels. (Depending on how well this improves performance, I may reimplement the secondary network search algorithm, as a side-option, which uses the same parallel-search within subarray strategies, as opposed to the primary network search algorithm that uses distance transforms).
-3. Image viewer window can now load in .nii format images, as well as .jpeg, .jpg, and .png. The nibabel library was added to the dependencies to enable .nii loading, although this is currently all it is used for (and the gui will still run without nibabel).
-4. Fixed bug regarding deleting edge objects. 
+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. 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.
+
+I do not anticipate any major updates for this project for the foreseeable future beyond bug fixes. 

{nettracer3d-0.5.3.dist-info → nettracer3d-0.5.5.dist-info}/RECORD

@@ -1,21 +1,21 @@
 nettracer3d/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nettracer3d/community_extractor.py,sha256=8bRDJOfZhOFLtpkJVaDQrQ4O8wUywyr-EfVvW5fxyPs,31700
+nettracer3d/community_extractor.py,sha256=Zq8ZM595CTzeR6zLEZ4I6KvhkNfCPUReWvAKxTlaVfk,33495
 nettracer3d/hub_getter.py,sha256=KiNtxdajLkwB1ftslvrh1FE1Ch9ZCFEmHSEEotwR-To,8298
 nettracer3d/modularity.py,sha256=V1f3s_vGd8EuVz27mzq6ycIGr0BWIpH7c7NU4QjgAHU,30247
 nettracer3d/morphology.py,sha256=yQ0GuieMVXOQpaohZlPnkEXEuCUjf8Fg352axyK8nbM,10755
-nettracer3d/nettracer.py,sha256=n3QLGPYiSGSYtsi-7scrhiW-GCS3scHljSbl46grZeY,209193
-nettracer3d/nettracer_gui.py,sha256=d5E4KP_-SB-Xs5IpgdXPsoBJoc8zgF5Z-sx2B2aWEHE,342672
+nettracer3d/nettracer.py,sha256=OE95IH1TfAZvT-htv1LEhw1EpnnEpkA83R5EcGMQDQg,209828
+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=Rr5MUUWgGHYzzTy4hzbO3zzJhNIKsyjV1Qxg99Pb8QY,29686
+nettracer3d/segmenter.py,sha256=hqe7VLRkil65d_KYyUwWbU7SbM7v-krVSeZfLUlHlfY,49587
 nettracer3d/simple_network.py,sha256=fP1gkDdtQcHruEZpUdasKdZeVacoLOxKhR3bY0L1CAQ,15426
 nettracer3d/smart_dilate.py,sha256=Kekm6YIVlJniMvJMG6_AwwNmCqK2l4Qtvg9VzzqPKMw,24600
-nettracer3d-0.5.3.dist-info/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
-nettracer3d-0.5.3.dist-info/METADATA,sha256=L17LXsiTk78oCeNyZXYonpmBWbI5Ys3zr2idCx-z4_o,4136
-nettracer3d-0.5.3.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-nettracer3d-0.5.3.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
-nettracer3d-0.5.3.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
-nettracer3d-0.5.3.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-0.5.3.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