From a794fbe32d1b2af539f0cec398efec7a29192908 Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Tue, 6 Sep 2016 11:18:37 +0200 Subject: No longer compensate for DIPHA dividing weights by 2. Version 0.0.6. --- README.md | 4 ++-- phstuff/diphawrapper.py | 33 ++++++++++++++++++--------------- setup.py | 2 +- 3 files changed, 21 insertions(+), 18 deletions(-) diff --git a/README.md b/README.md index b98470c..1e67fcf 100644 --- a/README.md +++ b/README.md @@ -35,8 +35,8 @@ following caveats: Installation ----- -Version 0.0.4 is available -[here](https://nonempty.org/software/python-phstuff/phstuff-0.0.4.tar.gz). The +Version 0.0.6 is available +[here](https://nonempty.org/software/python-phstuff/phstuff-0.0.6.tar.gz). The package can be installed using standard Python tools, for example by doing `python setup.py install --user` or something similar. diff --git a/phstuff/diphawrapper.py b/phstuff/diphawrapper.py index 4d1742e..1b633b5 100644 --- a/phstuff/diphawrapper.py +++ b/phstuff/diphawrapper.py @@ -29,10 +29,11 @@ def save_weight_matrix(fname, weights): """Write a NumPy weight matrix to a DIPHA full distance matrix file. Corresponds to DIPHA's "distance matrix data". - Attention: DIPHA uses a convention wherein an edge's - filtration value is *half* its weight. This function compensates - by multiplying every weight by 2. Pay attention in case DIPHA's - behavior changes in the future! + Attention: DIPHA currently uses a convention wherein an edge's + filtration value is *half* its weight. Prior to version 0.0.6 of + this package, we would compensate for this by multiplying every + weight by 2. As of version 0.0.6, we no longer do so. Pay + attention in case DIPHA's behavior changes in the future! Parameters: ----------- @@ -50,7 +51,7 @@ def save_weight_matrix(fname, weights): # we compensate by multiplying all entries by 2. Be sure to pay # attention if DIPHA's behavior changes! - factor = 2.0 + factor = 1.0 m = weights.shape[0] if weights.shape[0] != weights.shape[1]: @@ -73,10 +74,11 @@ def save_masked_weight_matrix(fname, weights): matrix file, keeping edges only for unmasked entries. Corresponds to DIPHA's "sparse distance matrix data". - Attention: DIPHA uses a convention wherein an edge's filtration - value is *half* its weight. This function compensates by - multiplying every weight by 2. Pay attention in case DIPHA's - behavior changes in the future! + Attention: DIPHA currently uses a convention wherein an edge's + filtration value is *half* its weight. Prior to version 0.0.6 of + this package, we would compensate for this by multiplying every + weight by 2. As of version 0.0.6, we no longer do so. Pay + attention in case DIPHA's behavior changes in the future! Parameters: ----------- @@ -89,7 +91,7 @@ def save_masked_weight_matrix(fname, weights): """ - factor = 2.0 + factor = 1.0 n = weights.shape[1] @@ -114,10 +116,11 @@ def save_edge_list(fname, edge_list): list to a DIPHA sparse distance file. Corresponds to DIPHA's "sparse distance matrix data". - Attention: DIPHA uses a convention wherein an edge's filtration - value is *half* its weight. This function compensates by - multiplying every weight by 2. Pay attention in case DIPHA's - behavior changes in the future! + Attention: DIPHA currently uses a convention wherein an edge's + filtration value is *half* its weight. Prior to version 0.0.6 of + this package, we would compensate for this by multiplying every + weight by 2. As of version 0.0.6, we no longer do so. Pay + attention in case DIPHA's behavior changes in the future! Parameters: ----------- @@ -139,7 +142,7 @@ def save_edge_list(fname, edge_list): """ - factor = 2.0 + factor = 1.0 n = len(edge_list) diff --git a/setup.py b/setup.py index ffa2007..4dc3ed7 100644 --- a/setup.py +++ b/setup.py @@ -1,7 +1,7 @@ from setuptools import setup setup(name="phstuff", - version="0.0.4", # Remember to update version and download + version="0.0.6", # Remember to update version and download # information in README.md too! description="Some persistent homology glue", url="https://nonempty.org/software/python-phstuff", -- cgit v1.2.3