From eb6c30a4a3700c8ac37c8ce30bcb7fd4766a89c4 Mon Sep 17 00:00:00 2001 From: alex-l-kong Date: Mon, 6 May 2024 14:11:33 -0700 Subject: [PATCH 1/3] Use more efficient ImzMLParserLite --- environment.yml | 1 + templates/maldi-pipeline.ipynb | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/environment.yml b/environment.yml index 3e235b6..0c6082e 100644 --- a/environment.yml +++ b/environment.yml @@ -15,4 +15,5 @@ dependencies: - matplotlib - pip: - alpineer + - git+https://github.com/angelolab/pyimzML.git - . diff --git a/templates/maldi-pipeline.ipynb b/templates/maldi-pipeline.ipynb index 3bffb46..9d41555 100644 --- a/templates/maldi-pipeline.ipynb +++ b/templates/maldi-pipeline.ipynb @@ -28,7 +28,7 @@ "import matplotlib.pyplot as plt\n", "import numpy as np\n", "import pandas as pd\n", - "from pyimzml.ImzMLParser import ImzMLParser\n", + "from pyimzml.ImzMLParser import ImzMLParser, ImzMLParserLite\n", "from maldi_tools import extraction, plotting" ] }, @@ -140,7 +140,7 @@ }, "outputs": [], "source": [ - "imz_data = ImzMLParser(data_path, include_spectra_metadata=\"full\")" + "imz_data = ImzMLParserLite(data_path)" ] }, { @@ -598,7 +598,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.1" + "version": "3.11.6" }, "vscode": { "interpreter": { From f82c45b920e45d2ba7f46740f2edb65b993f059b Mon Sep 17 00:00:00 2001 From: alex-l-kong Date: Mon, 6 May 2024 14:24:53 -0700 Subject: [PATCH 2/3] Downgrade pyimzml to be in line with forked version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index a93441d..cfe1bdf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ matplotlib = "^3.7.1" numpy = "^1.24.2" xarray = "^2023.2.0" pandas = "^1.5.3" -pyimzml = "^1.5.3" +pyimzml = "^1.5.1" scipy = "^1.10.1" scikit-image = "^0.20.0" tqdm = "^4.65.0" From d68f08ea45d4949e3858fca6730ce67138975c12 Mon Sep 17 00:00:00 2001 From: alex-l-kong Date: Mon, 6 May 2024 14:31:22 -0700 Subject: [PATCH 3/3] Update poetry.lock file --- poetry.lock | 2825 ++++++++++++++++++++++++++------------------------- 1 file changed, 1469 insertions(+), 1356 deletions(-) diff --git a/poetry.lock b/poetry.lock index 1cfe20b..c341b02 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. 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