diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 60cea951..cb0646bf 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -63,7 +63,6 @@ conda:build:windows: - win script: - conda activate base - - cd tools && git pull --force && cd.. - .\tools\build.bat conda:test:linux: diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml index 214919d5..bf6cdd00 100755 --- a/conda-recipe/meta.yaml +++ b/conda-recipe/meta.yaml @@ -33,6 +33,7 @@ requirements: - hdf5 - python - setuptools + - typing # [py27] - numpy run: - python diff --git a/doc/conf.py b/doc/conf.py index ff9ca692..15eea3b7 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -180,8 +180,7 @@ # index.html release_highlights_dir = Path("..") / "examples" / "release_highlights" # Finds the highlight with the latest version number -latest_highlights = sorted(release_highlights_dir.glob( - "plot_release_highlights_*.py"))[-1] +latest_highlights = sorted(release_highlights_dir.glob("plot_release_highlights_*.py"))[-1] latest_highlights = latest_highlights.with_suffix('').name html_context["release_highlights"] = \ f"auto_examples/release_highlights/{latest_highlights}" diff --git a/doc/templates/index.html b/doc/templates/index.html index 97d00551..20c66b18 100755 --- a/doc/templates/index.html +++ b/doc/templates/index.html @@ -102,15 +102,15 @@

time-tagged time-re
-

Photon distribution analysis

 -

Recover fluorescence lifetimes and distance distributions.

+

Photon distribution analysis

 +

Analyze intensities and recover distances.

Applications: Interaction studies, recover distances
Methods: MLE, and more...

- + Demonstration of a PDA
@@ -148,7 +148,7 @@

News

  • On-going development: What's new (Changelog) -
  • April 2021. tttrlib 0.21.2 is available for download (Changelog). +
  • January 2024. tttrlib 0.25.0 is available for download (Changelog).
  • tttrlib from 0.21 requires Python 3.8 or greater.
    • diff --git a/doc/themes/scikit-learn-modern/nav.html b/doc/themes/scikit-learn-modern/nav.html index 8054815e..d9237047 100755 --- a/doc/themes/scikit-learn-modern/nav.html +++ b/doc/themes/scikit-learn-modern/nav.html @@ -53,7 +53,7 @@ API
  • - Applications + Applications
    • {%- for title, link in drop_down_navigation %}
  • diff --git a/examples/tttr/plot_tttr_header.py b/examples/tttr/plot_tttr_header.py index d11f12b7..ecd9ae7b 100644 --- a/examples/tttr/plot_tttr_header.py +++ b/examples/tttr/plot_tttr_header.py @@ -24,7 +24,8 @@ """ import tttrlib -data = tttrlib.TTTR('./test/data/bh/bh_spc132.spc', 'SPC-130') + +data = tttrlib.TTTR('../../tttr-data/bh/pq/bh_spc132.spc', 'SPC-130') # the header can be accesses by the method get_header or as an property header = data.header @@ -40,10 +41,10 @@ # attribute modifies the header / meta data of a TTTR object. import json -data = tttrlib.TTTR('./test/data/PQ/PTU/PQ_PTU_HH_T3.PTU', 'PTU') +data = tttrlib.TTTR('./test/data/PQ/PTU/pq_ptu_hh_t3.ptu', 'PTU') #%% -# the header can be accesses by the method get_header or as an property +# the header can be accesses by the method get_header or as a property header = data.header header_json = header.json @@ -89,7 +90,7 @@ # Creating and writing TTTRHeader # =============================== # Each TTTR object has an attribute that is an instance of the TTTRHeader class. -# This instances makes the meta data contained in the TTTR file accessible. TTTRHeader +# This instances makes the meta-data contained in the TTTR file accessible. TTTRHeader # objects can also be created independently of TTTR object. header = tttrlib.TTTRHeader() @@ -105,7 +106,7 @@ #%% # The JSON string must contain a `tags` list. The `tags` list is a list of dictionarys -# in which each dictionary corresponds to a meta data field in the header. For instance, +# in which each dictionary corresponds to a meta-data field in the header. For instance, print(header.json) # '{\n "tags": []\n}' diff --git a/ext/python/Correlator.py b/ext/python/Correlator.py index 33f78cd5..a97a313c 100644 --- a/ext/python/Correlator.py +++ b/ext/python/Correlator.py @@ -14,7 +14,6 @@ def __getattr__(self, item): else: raise AttributeError - @property def correlation(self): return self.get_corr_normalized() diff --git a/pyproject.toml b/pyproject.toml index 2b94f074..85265e91 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -82,7 +82,6 @@ select = "cp3{8,9,10}-*" before-all = [ "yum update -y --nogpgcheck", - "yum update -y", "yum install -y epel-release", "yum -y install boost-devel swig cmake" ] diff --git a/src/TTTR.cpp b/src/TTTR.cpp index 325a978f..82de0d00 100644 --- a/src/TTTR.cpp +++ b/src/TTTR.cpp @@ -268,6 +268,9 @@ int TTTR::read_file(const char *fn, int container_type) { header = new TTTRHeader(fp, container_type); fp_records_begin = header->end(); tttr_record_type = header->get_tttr_record_type(); +#ifdef VERBOSE_TTTRLIB + std::clog << "-- TTTR record type: " << tttr_record_type << std::endl; +#endif processRecord = processRecord_map[tttr_record_type]; n_records_in_file = get_number_of_records_by_file_size( @@ -373,6 +376,9 @@ void TTTR::read_records( size_t chunk ) { n_rec = n_rec < n_records_in_file ? n_rec : n_records_in_file; +#ifdef VERBOSE_TTTRLIB + std::cout << "-- Records that will be read : " << n_rec << std::endl; +#endif if(rewind) fseek(fp, (long) fp_records_begin, SEEK_SET); // The data is read in two steps. In the first step bigger data chunks