Itk-montage

Changes:

* b5646c0d80ddde66850f48b76e46031f3e7e2de6 Merge pull request 153 from InsightSoftwareConsortium/wrap-all-classes
* 44c78689aa155372327b089e71076e95cb46fa67 COMP: Make TileMergeImageFilter::ContinuousIndexType more explicit
* 912f433f5aa5be3b4d46df2bf445c9c4b764b088 Merge 704dc56219cd912a22e4ebf3c44da83798589c9b into eba24acb3981bc02d6498d30481d7ebc0ad752be
* 3a6e3b960fbeecaae65da3c5e6881e6d3547efcd COMP: NMinimaMaximaImageCalculator initialization
* 824bf3434848f79838128444fc8accbeacbfab30 COMP: Patch igenerator.py for enum wrapping
* e7da790f548c80e0688bfd45e5ecae8e75f5352e ENH: Add TileMergeImageFilter wrapping
* c65afeef7a5f35e0975d2fc07908552a8b6ca908 ENH: Add TileMontage wrapping
* 142eaa10408493efb536725e131a7dfef77c07a6 ENH: Wrap Tile, TileConfiguration
* 5a2cd37d5ff50e7101569fe1ab4152eff878fff3 ENH: Add wrapping for NMinimaMaximaImageCalculator
* 00860e627e74d67caf53b20b80e3879bc6bc0878 ENH: Wrap MaxPhaseCorrelationOptimizer
<details><summary><b>See More</b></summary>

* 7985d7ced42f4b77fa18273013217065a642a826 ENH: Wrap PhaseCorrelationImageRegistrationMethod for all scalar pixel types
* 025f69ce06136d3a0aebe62721ef3f5dfe96508f ENH: Restrict Python package dependencies
* d0158bab83d0d9c50c6195605dee8f97619ae324 ENH: Add clang-format GitHub Actions
* 010b364492c11e4833af56ccb7be01a25681948e ENH: Add .gitattributes
* 6cb85beb86ce7360fd54dddecacc194e070e3edc STYLE: Apply clang-format for ITK Coding Style
* a240939ae8ee1153b4ec4f45cfe68f542a1a537c ENH: Remove CircleCI configuration
* eba24acb3981bc02d6498d30481d7ebc0ad752be Merge pull request 151 from InsightSoftwareConsortium/package-dependencies
* 5cab5161a086d375613bacfbb6d6604b783cd8d9 ENH: Restrict Python package dependencies
* 5dfc3c0ef58d5cdfacf26eaeae9bb5d7bc11b374 Merge pull request 148 from InsightSoftwareConsortium/style-hooks
* af383deb228b10646f7acda4c679ef2421788c19 Merge pull request 149 from thewtex/remove-circle-ci
* 0bd13d44c3740e4972ca12b4d28dfe90c5dedc0c Merge pull request 150 from thewtex/python-package-version
* a7c9525a1ad59c9c61590a85a0d5e46fdfc65a8f ENH: Bump Python package version to 0.5.0
* 1771da2d9ef9fad7960be4cf653700d87927bcdf ENH: Remove CircleCI configuration
* f376a889f617ad01b64c36e544b207bc23e4b244 Merge pull request 147 from thewtex/readme-badges
* b90a1667ed1f540d9b2e9a7f64d1169b163042dc ENH: Add clang-format GitHub Actions
* 3d4ddbdd2bc2ac2d03db9d560ad2161421016b68 ENH: Add .gitattributes
* ff88e8fa47d29ed817202a87901df83a0db54a6c STYLE: Apply clang-format for ITK Coding Style
* a0440daf161d76d89e01c28b94745ce5b708b582 DOC: Fix README badges
* def98ac12145213c49f50a56bcb21c49284a6316 Merge pull request 145 from dzenanz/master
* c8e68a81ce624d01d932023ae92fa4ea2fe3a480 STYLE: better formatting
* 5896493efdf966d3de8ce97a85abbd6b8fda2fe1 ENH: do not force full parallelism
* bfe68e9c44e91c5a72ba8efe6c76085e3c6964f9 BUG: position of tile 0 was not subtracted for origin adjustment
* 06939f64f114692531d1b66ef2c0d701c841134d BUG: ITK_USE_FFTW definitions were not propagated in external builds
* 03643b41a0766f4dec3255005002bb8a2cc76b4e Merge pull request 144 from dzenanz/master
* 9e545f06e2196fcbbb4a0dfd7eb00077d3314147 BUG: fix AxisSize when final dimension is 1
* cb48757f1dee84031ba0e8da2bd3ddb1708f278f ENH: add a fake input data file to make the configurations valid
* d4420e5cae9c459ddb7113e340686d20d0992c90 ENH: add single-layer 3D test which currently crashes
* da0c79c75c22045cce9f402af2e50eaff5719e6c Merge pull request 142 from dzenanz/master
* fdaa88bd03fe55f68a1ac2b9f7f2481693f42d1c ENH: update ITK version in CI testing infrastructure
* 952c6cede6d22e2b84baf8f26f1d962fcb451db2 COMP: follow rename of ImageIOFactory FileModeType into FileModeEnum
* 62ed2415126ad824ba519e36a94544aa7afb9e37 Merge pull request 138 from dzenanz/master
* c5b7fec7b4c835be5f8885d7245c7d09f637f39d COMP: fixing warnings
* d6544075a0838d6df2fb14b566522c3fec2c0876 Merge pull request 136 from dzenanz/master
* 9242f88a672b877a5634f229bdc08059cc1169da ENH: better error reporting in GroundTruthCreator
* 08f3380df1cd51932d1ff2722ec4e7f8b6030dbd ENH: better exception reporting in test
* da2bdf92f7da8878c202e79d24f9174e65c48aa3 BUG: 1701701_000000_Fused is in TIF format
* 9fd219b2ec70837788021259d4cb239e53d6d5c2 BUG: fix buffer overflow on float to string conversion
* 969d071933635c58af5926c5e17a1883a1e6db2a COMP: fixing example compile warnings on GCC 5.4.0
* bf9414d3973f6900f234db24ac92432ae89036b7 COMP: fixing in-source build of the examples
* fa1b5875b1e8d5739fdce51013032e81823e361e COMP: adding a few missing typenames
* f7b6eaf99a1a7f49a874be25e91bb423c285a8f6 Merge pull request 135 from dzenanz/master
* 5a2535dc1ed6e95e004b6d192adb6fe4573bcf4b ENH: add calculation of systematic translation bias to pair-wise test [ 52, 54, 56, 70, 79 ]
* b38bf1ca7e29031f77e64e43a22bca80fd9dacca Merge pull request 134 from dzenanz/master
* ffc3dfedf2188d9fe42e770c214807ff6a349717 ENH: add noise reduction step to the complete example
* de7e3f10427f5c1d4861f2f13233299b29451896 ENH: resolving TODOs
* a75f1c22be9fc43937d26c83a6b3486128b82750 ENH: add 3D test for CompleteMontage
* 974037bd725241971ea93c97a48b483761ff704b ENH: write bias-corrected images
* 3cd571623ba18da8e27e39554ec73d020ea1515d ENH: adding bias field correction to the complete example
* 4d28b156df743314043c4075a68f92b499776b25 ENH: read images just once
* fd31fef4dcf2d3f3ac6d15f453e92ffdfd7446be ENH: Removing Parse/Write TileConfiguration2D
* fec3c596c114a713da6ce0b2b13b831a6bbe8f10 ENH: updating examples to work with nD montages
* fd446f7c676ea1c2c5c1104ee9217fe88c7e1d0f ENH: add 3D sample data to examples (from ground truth creator)
* da29f315f4e085d0bd01caf55e4032830131805d ENH: add 2D sample data to examples (from ground truth creator)
* e5e8dfe9dea0ba24fac5a7b382bde8870260d6a9 ENH: add ImageCompareCommand.cxx from ITKExamples
* 5aad8d185da8679f14b55f03fb8312012c52a538 ENH: add TileConfiguration comparison tool
* f357b8059aa00b8fcadb2d1d1c00fc1949c6a7fb STYLE: remove 2D from example names
* 708c7cf0b0cd0c96de70505a81e7b0bed920c86d Merge pull request 133 from dzenanz/updateInMemoryTest
* 0be6f4ba5285a897ab2e1a5543b27475346e9337 ENH: Update InMemoryMontageTest to use nD structure
* c2cbbc1414c455e32e0e8727bbe71483301bdadb Merge pull request 132 from dzenanz/master [ 127 ]
* 7799472d66fd80374c805fd4fa5862481b0caa6c ENH: support multi-dimensional tile configuration. Closes 127.
* 05d428f1670017b621a0833d080b10e110daf4b3 Merge pull request 130 from dzenanz/master
* 8eb0e8474e6643532540b6cb747f0a5b82953607 STYLE: converting README.rst into README.md. Closes 128.
* 8d2078d1dc1a9b350989788a1d1547796b5a8190 STYLE: rename itkParseTileConfiguration into itkTileConfiguration
* 35211ac817ef7b482c9b67c03e058ab83486f6d7 STYLE: manual fix of KWSTyle alignment error
* 927da909fa7b66aff25335b58b6e1cf7e38a4870 STYLE: fixing KWStyle error
* 72004082dbd21f28dee94dfb8ee19a81a85e9d99 STYLE: applying new ITK style
* ef24b5c31ec64837ba806fa458f85b0da6d5d64e STYLE: update clang-format style to follow recent ITK change
* 9bbe940b7c79031f75cbac952ba0c11413605fe5 Merge pull request 129 from mseng10/enh-move-enum-class-modules
* aafb88c8ade26c67ba1e2aa65905c7af8f5a85a5 COMP: Change to enum to new enum class definitions
* 1ee67f1a09767de39836e97466c602828ec8eb05 Merge pull request 126 from dzenanz/master
* ffe9f509c240f9cec39d7b0f7093509aa4545b2c ENH: add 3D ground truth case
* a09fb1d2b7cd14cc2aecb389a9688548c584253e BUG: conversion from linear to nD index was wrong for 3D montages
* 0169b7e7b78a0f5381e8c5306c033bdbdf389a37 BUG: file opening was not checked for success. Closes 122.
* 4849a8b929eabb58a1533fb7eb63e3a873119eb0 Merge pull request 125 from dzenanz/master
* 8337940cb4591bace3d80f3846b35818d8c8285f ENH: update ITK to support RGB in WindowedSinc interpolator
* ed95875b121046e0c895a86a9e35ce243525edd5 ENH: WindowedSincInterpolateImageFunction for better resampling quality
* bdad60afc550adf765c505cfbb9c49376b1339f8 ENH: adding ground truth creator. Closes 108.
* 58b3e0664e79e048469ee8b1888483a67d41a31e BUG: Old .bmp named file was a TIFF
* 02be33ab97e457c4af18ecdd934b326e2511c5ed COMP: fix unused variable warning

This list of changes was [auto generated](https://dev.azure.com/ITKMontage/20af96ed-85f3-43ef-a753-aee2fd0f4f10/_release?releaseId=27&_a=release-summary).</details>

Changes:

* d48b400cea8d96f1db51829f0d3a6596e4da2c78 Merge pull request 123 from thewtex/python-itk-5.0.1
* 6e45b271a8fe023ee73af7734233db4ce37b6004 DOC: Document installation
* 803670c452cc856e2ec4186c2cbe2876e909c6f7 ENH: Build Python package against ITK 5.0.1

This list of changes was [auto generated](https://dev.azure.com/ITKMontage/20af96ed-85f3-43ef-a753-aee2fd0f4f10/_release?releaseId=6&_a=release-summary).

Changes:

* e6ba4d41922073abc5e6345aec69e015300ce440 Merge pull request 121 from thewtex/python-package-0.4.0
* a85a56be1c14a299c068d95a7ee4f9a61d7a3a29 ENH: Bump Python package version to 0.4.0
* d794c2d3b97551e195f129920c407e3a9ab96199 Merge pull request 118 from dzenanz/master
* 64f87515c9ce602acba98946b05e35abd293fd49 ENH: checking whether interpolation is needed
* 8f5e59ec8b5b4ace3caabe17e264e107f4e9b6a9 ENH: increase parallelism and cache tiles
* 14bd397ab8840536df93b0ca777a60e0b80d607e ENH: parallel generation of synthetic sphere image
* 27fc61d19aa4c7a49aed451a14447cafe245ed06 Reduce majority of duplication in synthetic tests
* 78cc5a36105cf7b089ff5dd83b35ab0a4919a2eb COMP: ITK testing macros have ITK_ prefix since version 5.0+
* c547a1f289abdf672756790a7f3a1930ceb8df21 Merge pull request 120 from thewtex/azure-config
* 9578964ddab7dbfecf3d81828d8fa97746764551 ENH: Bump CI ITK Git commit to 2019-07-23 master
<details><summary><b>See more</b></summary>

* 1717965a24310d156b131c6c143109b210494aba ENH: Support arbitrary ITK C++ Git commit in Azure
* 13425fb96c22f3b0ed853d1822759cbfe9174378 ENH: Remove Travis config
* b7a3c4e72b8c8c638ecf94551377d3a27afd7482 ENH: Update Azure Pipelines configuration to support ITKPythonGitTag
* 3b64b8d8497fbaf0b5c7e779a08ce63fe8365645 Merge pull request 119 from thewtex/azure-config
* d1dc09a843f38e33b64ac3fc2aaa7d18facb0e86 DOC: Update Azure pipeline badge
* bbcbaa6e0205655a9bd01f1c1f0dfe5da6b226c0 Merge pull request 116 from dzenanz/master
* 3be92c8d12b97cc01233fdceac7103342921859c ENH: adding github.io as an alternative source for testing data
* 7897e209291dd03ae544a96e117db926272ab351 ENH: all tests write their result except S200
* 7ea4a792cfa07009603fed94b51346a7fb05cdb8 ENH: the stitched mosaic does not have to be written
* 4ea099560e727ce24aca6d70c557e2edf2e7b6ae ENH: change parameters of large tests to reduce peak memory use
* 3bfc18875cbbf71f6666b877c531dfaea722d81b ENH: only two tests still fail
* 7419a2750cfb9ebcb9a04f45e01c9fce9f769d9d STYLE: avoid specifying ITK namespace when already inside it
* 261c119e5419bec23521c834275bd93a609439e7 ENH: output indication of failing tile and average error to TSV file
* 97c57ae072132da1b3a8e0ab7d84cc9b31e93bb6 ENH: more granular progress reporting (per pair, not per tile)
* d13383b7eaec19c4323b1e709ad3b3d62085701a ENH: use registration confidence in equations and cost
* 3e6cbe6d3025f5b99d1a670407c99ee3a0598750 BUG: residuals were not properly divided by spacing
* dd081ac1cea49af9dab9809f38be76c19bcbe931 ENH: allowing specification of real type used in FFTs
* d1769f73594cae367cdcf08be1ecaabf7d0f5a76 STYLE: simplifying type specification
* b0c1320614c6015e527405f135590ae1d6d161c4 ENH: allow more low frequencies to pass by default
* 98127ddbabc113571a1947ce5a6226cd32976104 BUG: fix and slightly optimize zero suppression
* 0d03c180fce71630d3fe132467fdff52d154e625 BUG: merge peak distance was not respected (1 was always used)
* 961d2c68fd98b220d95d276a813bba43da156150 BUG: better message for wrong number of parameters
* f0e4e7910f8c4faeb945c84177d426b9f017febd ENH: adding problematic S200 pairs as separate tests
* b84e11a91e7a3b750af6f93c344ef7683df3fee2 ENH: more informative outlier reporting
* 69a9217c0b2a890a568c66fc4b15ac46dd3b88d5 ENH: prevent translations being rejected simply for being large
* b0ae3cb74fa7ccb9da929f9ee471c76da62eece1 ENH: make zero suppression more consistent and less pronounced
* b6dada0d863f3c5728e574a4e1d55a4296a5d53c ENH: do zero suppression only if needed
* f37e346ea56086ae9d91a846584590b2df8a1ba9 BUG: I forgot to update sheet/line zero suppression formula
* a886015764971e8c3c9c591f86d078efa6ddb27c ENH: adding first registration pair of 10-129-C_2 as a separate test
* 9ee84b1a630f47a89926be9152ce826fdaea3dc1 ENH: allow drift for MNML5
* f1f82acc2daa0e208876411520dc4bd4e484df20 BUG: fix wrong test parameters
* d4c30dae3d8c94f24d187367484d767e0e70ca4c ENH: expand the cropping region
* 975b2fe64159c5d600ef2655f0ffc6c07f374f98 ENH: crop images to overlapping portion for cross-correlation [ 95 ]
* aa7c588f63ee2c91ed962da9d1837b634585052e ENH: write input images after FFT band-pass filtering

This list of changes was [auto generated](https://dev.azure.com/ITKMontage/20af96ed-85f3-43ef-a753-aee2fd0f4f10/_release?releaseId=4&_a=release-summary).</details>

Changes:

* 1962de8ab6a00eb698a5a3716a9c6d5d04eb167d Merge pull request 113 from dzenanz/positionTolerance
* 7836d27506b71055f3ae85886eb817d418d15e0d ENH: reduce evaluations of exp function
* f485254b46a62bcde7235f6945e725dcc5cb4644 ENH: use tile position tolerance in tests. Closes 105.
* 316d698ebaa798b60cd7247d8c3f967c261336e3 ENH: rewrite position tolerance to be expressed in pixels
* 3b8b339ffa2e5e8e45fbc3564f744cca998fcfe2 ENH: expose position precision in TileMontage class
* 24a138971490835a114ae3fc69ee29c06db56f33 BUG: fix re-ordering of peak maxima during zero suppression
* f15d37b1beb865fa6ef8b904d06dc2f27677c5a7 Merge pull request 112 from dzenanz/globalOptimization
* 99e64ce9e7e3090309c9ec8dd17fc4e4799c7682 Merge pull request 111 from thewtex/azure-configuration-update
* 33fd81e25045371fb69dc88328e314e35f0b52aa STYLE: review suggestions
* 7524d31d24b18a474b8a22cdea839d80610fb9ac ENH: Update CI Build to build against 5.0.0.post1
<details><summary><b>See more</b></summary>

* 85be4cd67b103cdc4ab9083a1995d2b1d7a08e8f ENH: move more test to expected to pass category
* a39d3eeb3f234f21003cb5361a90c605af95b28b ENH: use translation offsets instead of transforms internally
* c1c1cd731a41151614e04b35243b1d29f9a97b70 STYLE: remove empty space in example
* e85254e1aae170cf069f41cb07fc0ddb305d1a1c ENH: update examples to support non-unit spacing
* 267148dc698f8a093e4992d5167ffe9fc52f4db6 ENH: increase test success threshold from 1.0 to 1.2 pixels
* 94bba05cf6ab3079671780b4bd4cce11571847e0 ENH: global optimization with outlier detection and removal
* 1040001806daa4e2126d1f6678d44ec9da9b7194 Merge pull request 110 from dzenanz/testImprovements
* 3016358153e9fbb29c0289bc84126b6b4999b791 ENH: expose allowing accumulation of errors (drift) in tests
* 22d896f5d2cdea502a00a4c181ab772b6025674b ENH: reorganizing test names and output locations
* d2008f49b85ad9b602c6cb1565f4d8e70480261a ENH: Ti64 tests are no longer failing
* 00a8190bd33290663c736202773bcb6a89153a7f ENH: account for accumulation of errors
* 6c55623e66c59c1ffd5668e976d6aee9bb8b97d2 BUG: fix calculation of average tile displacement error
* 4826a54323237745495309659919654e54771e88 BUG: correctly offset translations by position of tile 0
* 34aba30fd4f0261fcb4b9627c8de05fb13e4c403 ENH: add the problematic region of S200 as a standalone test case
* d578632d07d8b609acdaa22e8cb4ef3c89437f2d ENH: adding 05MAR09_run2_64-Raw test data from CMU
* b69b5d7cfcb1e70cd2502319238404a14b03d143 ENH: Adding Medium Carbon Steel 1701701_000000 test (UES corporation)
* 2ee68760bc015b5b7c521ec0526c2f2290574103 ENH: adding Ti7/Region1_10_Mosaic36 and Ti7/Region1_10_Mosaic180 tests
* 28dfb865a7509db9127de1452b6a5cd7aea0a798 STYLE: rename directory of Ti7Al test case
* bc466958b0f17b6cbf39920c40cf7fcb7fcabe93 BUG: cosine interpolation avoids NaNs for additional candidates
* a70d7b617bd297e3adfd4d95a5b2ea46c343c663 ENH: do not require unnecessary maxima
* dd8735b5ddc63bd28d2a9bfa434d4293b845e1c2 Merge pull request 107 from dzenanz/minorUpdates
* e239308299b510120c4120b3f8702edb79d42a0e ENH: Build against ITK 5.0.0 and bump Python package version
* 7954e5f115843539bb77948b5f78b69fae1c5c93 BUG: with peak merging enabled a peak can have a brighter pixel nearby
* 8560561281c530a8a16414115d923ab12602c018 DOC: expose transform writing in usage

This list of changes was [auto generated](https://dev.azure.com/InsightSoftwareConsortium/589c7c69-a644-4c41-8c80-35e059deabd5/_release?releaseId=98&_a=release-summary).</details>