From 3868c3e0a85c5aa34092968d3d885b8bc5482307 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Tue, 17 May 2022 17:47:01 +0100
Subject: [PATCH] add local Image and update poetry deps

---
 aliby/io/image.py | 107 ++++++
 aliby/io/omero.py |  35 --
 poetry.lock       | 840 ++++++++++++++++++++++++----------------------
 pyproject.toml    |   8 +-
 4 files changed, 560 insertions(+), 430 deletions(-)
 create mode 100644 aliby/io/image.py

diff --git a/aliby/io/image.py b/aliby/io/image.py
new file mode 100644
index 00000000..ded8d8b9
--- /dev/null
+++ b/aliby/io/image.py
@@ -0,0 +1,107 @@
+#!/usr/bin/env python3
+
+from aliby.experiment import get_data_lazy_local
+from pathlib import Path
+from tifffile import TiffFile
+from pathlib import Path
+import xmltodict
+from aliby.experiment import get_data_lazy
+from aliby.io.omero import Argo
+
+
+class ImageLocal:
+    def __init__(self, path: str):
+        self.path = path
+        self.image_id = str(path)
+
+        try:
+            with TiffFile(fpath) as f:
+                self.meta = xmltodict.parse(f.ome_metadata)["OME"]
+            meta = dict()
+            for dim in self.dimorder:
+                meta["size_" + dim.lower()] = int(
+                    self.meta["Image"]["Pixels"]["@Size" + dim]
+                )
+            meta["channels"] = [
+                x["@Name"] for x in self.meta["Image"]["Pixels"]["Channel"]
+            ]
+            meta["name"] = self.meta["Image"]["@Name"]
+            meta["type"] = self.meta["Image"]["Pixels"]["@Type"]
+
+            self._meta = meta
+
+        except Exception as e:
+            # TODO implement default meta when no image metadata
+            print("Could not fetch metadata: {}".format(e))
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, *exc):
+        return False
+
+    @property
+    def name(self):
+        return self._meta["name"]
+
+    @property
+    def data(self):
+        return self.get_data_lazy_local()
+
+    @property
+    def dimorder(self):
+        """Order of dimensions in image"""
+        return self.meta["Image"]["Pixels"]["@DimensionOrder"]
+
+    @property
+    def metadata(self):
+        return self._meta
+
+    def get_data_lazy_local(self) -> da.Array:
+        """Return 5D dask array. For lazy-loading local multidimensional tiff files"""
+        return da.rechunk(
+            imread(str(self.path))[0],
+            chunks=(1, 1, 1, self._meta["size_y"], self._meta["size_x"]),
+            # chunks="auto",
+        )
+
+
+class Image(Argo):
+    """"""
+
+    def __init__(self, image_id, **server_info):
+        super().__init__(**server_info)
+        self.image_id = image_id
+        self._image_wrap = None
+
+    @property
+    def image_wrap(self):
+        # TODO check that it is alive/ connected
+        if self._image_wrap is None:
+            self._image_wrap = self.conn.getObject("Image", self.image_id)
+        return self._image_wrap
+
+    # Version with local file processing
+    def get_data_lazy_local(path: str) -> da.Array:
+        """Return 5D dask array. For lazy-loading local multidimensional tiff files"""
+        return da.from_delayed(imread(str(path))[0], shape=())
+
+    @property
+    def name(self):
+        return self.image_wrap.getName()
+
+    @property
+    def data(self):
+        return get_data_lazy(self.image_wrap)
+
+    @property
+    def metadata(self):
+        meta = dict()
+        meta["size_x"] = self.image_wrap.getSizeX()
+        meta["size_y"] = self.image_wrap.getSizeY()
+        meta["size_z"] = self.image_wrap.getSizeZ()
+        meta["size_c"] = self.image_wrap.getSizeC()
+        meta["size_t"] = self.image_wrap.getSizeT()
+        meta["channels"] = self.image_wrap.getChannelLabels()
+        meta["name"] = self.image_wrap.getName()
+        return meta
diff --git a/aliby/io/omero.py b/aliby/io/omero.py
index 622bebfc..8fa8ed9a 100644
--- a/aliby/io/omero.py
+++ b/aliby/io/omero.py
@@ -6,7 +6,6 @@ from agora.io.cells import CellsHDF
 
 
 class Argo:
-    # TODO use the one in extraction?
     def __init__(
         self, host="islay.bio.ed.ac.uk", username="upload", password="***REMOVED***"
     ):
@@ -94,40 +93,6 @@ class Dataset(Argo):
         return True
 
 
-class Image(Argo):
-    def __init__(self, image_id, **server_info):
-        super().__init__(**server_info)
-        self.image_id = image_id
-        self._image_wrap = None
-
-    @property
-    def image_wrap(self):
-        # TODO check that it is alive/ connected
-        if self._image_wrap is None:
-            self._image_wrap = self.conn.getObject("Image", self.image_id)
-        return self._image_wrap
-
-    @property
-    def name(self):
-        return self.image_wrap.getName()
-
-    @property
-    def data(self):
-        return get_data_lazy(self.image_wrap)
-
-    @property
-    def metadata(self):
-        meta = dict()
-        meta["size_x"] = self.image_wrap.getSizeX()
-        meta["size_y"] = self.image_wrap.getSizeY()
-        meta["size_z"] = self.image_wrap.getSizeZ()
-        meta["size_c"] = self.image_wrap.getSizeC()
-        meta["size_t"] = self.image_wrap.getSizeT()
-        meta["channels"] = self.image_wrap.getChannelLabels()
-        meta["name"] = self.image_wrap.getName()
-        return meta
-
-
 class Cells(CellsHDF):
     def __init__(self, filename):
         file = h5py.File(filename, "r")
diff --git a/poetry.lock b/poetry.lock
index 2d334d87..fdd597af 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -78,7 +78,7 @@ python-versions = "*"
 
 [[package]]
 name = "aliby-agora"
-version = "0.2.22"
+version = "0.2.25"
 description = "A gathering of shared utilities for the Swain Lab image processing pipeline."
 category = "main"
 optional = false
@@ -94,14 +94,16 @@ PyYAML = ">=6.0,<7.0"
 
 [[package]]
 name = "aliby-baby"
-version = "0.1.7"
+version = "0.1.8"
 description = "Birth Annotator for Budding Yeast"
 category = "main"
 optional = false
 python-versions = ">=3.7.1,<3.11"
 
 [package.dependencies]
+colorama = ">=0.4.4,<0.5.0"
 imageio = "2.8.0"
+keras-tuner = "1.0.1"
 matplotlib = ">=3.5.1,<4.0.0"
 numpy = ">=1.16.0,<2.0.0"
 pandas = ">=1.1.4"
@@ -116,18 +118,20 @@ xgboost = "1.4.2"
 
 [[package]]
 name = "aliby-post"
-version = "0.1.21"
+version = "0.1.25"
 description = "Post-processing tools for aliby pipeline."
 category = "main"
 optional = false
 python-versions = ">=3.7.1,<3.11"
 
 [package.dependencies]
-aliby-agora = ">=0.2.22,<0.3.0"
+aliby-agora = ">=0.2.25,<0.3.0"
 catch22 = ">=0.2.0,<0.3.0"
+gaussianprocessderivatives = ">=0.1.2,<0.2.0"
 leidenalg = ">=0.8.8,<0.9.0"
 more-itertools = ">=8.12.0,<9.0.0"
 numpy = ">=1.17.3"
+p-tqdm = ">=1.3.3,<2.0.0"
 pandas = ">=1.1.4,<2.0.0"
 pathos = ">=0.2.8,<0.3.0"
 PyYAML = ">=6.0,<7.0"
@@ -267,7 +271,7 @@ python-versions = "*"
 
 [[package]]
 name = "charset-normalizer"
-version = "2.0.11"
+version = "2.0.12"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 category = "main"
 optional = false
@@ -278,11 +282,11 @@ unicode_backport = ["unicodedata2"]
 
 [[package]]
 name = "click"
-version = "8.0.3"
+version = "8.1.0"
 description = "Composable command line interface toolkit"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
@@ -382,7 +386,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
 name = "filelock"
-version = "3.4.2"
+version = "3.6.0"
 description = "A platform independent file lock."
 category = "main"
 optional = false
@@ -394,7 +398,7 @@ testing = ["covdefaults (>=1.2.0)", "coverage (>=4)", "pytest (>=4)", "pytest-co
 
 [[package]]
 name = "fonttools"
-version = "4.29.1"
+version = "4.31.2"
 description = "Tools to manipulate font files"
 category = "main"
 optional = false
@@ -423,11 +427,11 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "fsspec"
-version = "2022.1.0"
+version = "2022.2.0"
 description = "File-system specification"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.extras]
 abfs = ["adlfs"]
@@ -467,9 +471,22 @@ category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[[package]]
+name = "gaussianprocessderivatives"
+version = "0.1.4"
+description = "Uses Gaussian processes to smooth data and estimate first- and second-order derivatives"
+category = "main"
+optional = false
+python-versions = ">=3.7.1,<3.11"
+
+[package.dependencies]
+matplotlib = ">=3.5.1,<4.0.0"
+numpy = ">=1.16.0,<2.0.0"
+scipy = ">=1.7.3,<2.0.0"
+
 [[package]]
 name = "google-api-core"
-version = "2.5.0"
+version = "2.7.1"
 description = "Google API client core library"
 category = "main"
 optional = false
@@ -533,7 +550,7 @@ six = "*"
 
 [[package]]
 name = "googleapis-common-protos"
-version = "1.54.0"
+version = "1.56.0"
 description = "Common protobufs used in Google APIs"
 category = "main"
 optional = false
@@ -564,7 +581,7 @@ test = ["mock (>=2.0.0)", "pytest (<5.0)"]
 
 [[package]]
 name = "grpcio"
-version = "1.43.0"
+version = "1.45.0"
 description = "HTTP/2-based RPC framework"
 category = "main"
 optional = false
@@ -574,7 +591,7 @@ python-versions = ">=3.6"
 six = ">=1.5.2"
 
 [package.extras]
-protobuf = ["grpcio-tools (>=1.43.0)"]
+protobuf = ["grpcio-tools (>=1.45.0)"]
 
 [[package]]
 name = "h5py"
@@ -641,7 +658,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "importlib-metadata"
-version = "4.10.1"
+version = "4.11.3"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
@@ -652,24 +669,24 @@ typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
 perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
 
 [[package]]
 name = "importlib-resources"
-version = "5.4.0"
+version = "5.6.0"
 description = "Read resources from Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy"]
+docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
 
 [[package]]
 name = "iniconfig"
@@ -681,11 +698,11 @@ python-versions = "*"
 
 [[package]]
 name = "jinja2"
-version = "3.0.3"
+version = "3.1.1"
 description = "A very fast and expressive template engine."
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 MarkupSafe = ">=2.0"
@@ -752,24 +769,49 @@ image = ["scipy (>=0.14)", "Pillow (>=5.2.0)"]
 pep8 = ["flake8"]
 tests = ["pandas", "pillow", "tensorflow (==1.7)", "keras", "pytest", "pytest-xdist", "pytest-cov"]
 
+[[package]]
+name = "keras-tuner"
+version = "1.0.1"
+description = "Hypertuner for Keras"
+category = "main"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+colorama = "*"
+future = "*"
+numpy = "*"
+requests = "*"
+scikit-learn = "*"
+scipy = "*"
+tabulate = "*"
+terminaltables = "*"
+tqdm = "*"
+
+[package.extras]
+tests = ["pytest", "flake8", "mock", "portpicker", "pytest-xdist", "pytest-cov"]
+
 [[package]]
 name = "kiwisolver"
-version = "1.3.2"
+version = "1.4.2"
 description = "A fast implementation of the Cassowary constraint solver"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
+[package.dependencies]
+typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
+
 [[package]]
 name = "leidenalg"
-version = "0.8.8"
+version = "0.8.9"
 description = "Leiden is a general algorithm for methods of community detection in large networks."
 category = "main"
 optional = false
 python-versions = "*"
 
 [package.dependencies]
-python-igraph = ">=0.9.0"
+igraph = ">=0.9.0,<0.10"
 
 [[package]]
 name = "locket"
@@ -795,11 +837,11 @@ testing = ["coverage", "pyyaml"]
 
 [[package]]
 name = "markupsafe"
-version = "2.0.1"
+version = "2.1.1"
 description = "Safely add untrusted strings to HTML/XML markup."
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "matplotlib"
@@ -927,7 +969,7 @@ signedtoken = ["cryptography (>=3.0.0)", "pyjwt (>=2.0.0,<3)"]
 
 [[package]]
 name = "omero-py"
-version = "5.11.0"
+version = "5.11.1"
 description = "Python bindings to the OMERO.blitz server"
 category = "main"
 optional = false
@@ -976,7 +1018,7 @@ numpy = ">=1.13.3"
 
 [[package]]
 name = "opencv-python"
-version = "4.5.5.62"
+version = "4.5.5.64"
 description = "Wrapper package for OpenCV python bindings."
 category = "main"
 optional = false
@@ -1003,6 +1045,19 @@ numpy = ">=1.7"
 docs = ["sphinx (==1.2.3)", "sphinxcontrib-napoleon", "sphinx-rtd-theme", "numpydoc"]
 tests = ["pytest", "pytest-cov", "pytest-pep8"]
 
+[[package]]
+name = "p-tqdm"
+version = "1.3.3"
+description = "Parallel processing with progress bars"
+category = "main"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+pathos = "*"
+six = "*"
+tqdm = "*"
+
 [[package]]
 name = "packaging"
 version = "21.3"
@@ -1109,7 +1164,7 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "platformdirs"
-version = "2.5.0"
+version = "2.5.1"
 description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "dev"
 optional = false
@@ -1304,26 +1359,9 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 [package.dependencies]
 six = ">=1.5"
 
-[[package]]
-name = "python-igraph"
-version = "0.9.9"
-description = "High performance graph data structures and algorithms (legacy package)"
-category = "main"
-optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-igraph = "0.9.9"
-
-[package.extras]
-cairo = ["cairocffi (>=1.2.0)"]
-matplotlib = ["matplotlib (>=3.3.0)"]
-plotly = ["plotly (>=5.3.0)"]
-plotting = ["cairocffi (>=1.2.0)"]
-
 [[package]]
 name = "pytz"
-version = "2021.3"
+version = "2022.1"
 description = "World timezone definitions, modern and historical"
 category = "main"
 optional = false
@@ -1331,7 +1369,7 @@ python-versions = "*"
 
 [[package]]
 name = "pywavelets"
-version = "1.2.0"
+version = "1.3.0"
 description = "PyWavelets, wavelet transform module"
 category = "main"
 optional = false
@@ -1399,16 +1437,18 @@ tune = ["pandas", "tabulate", "tensorboardx"]
 
 [[package]]
 name = "redis"
-version = "4.1.3"
+version = "4.2.0"
 description = "Python client for Redis database and key-value store"
 category = "main"
 optional = false
 python-versions = ">=3.6"
 
 [package.dependencies]
+async-timeout = ">=4.0.2"
 deprecated = ">=1.2.3"
 importlib-metadata = {version = ">=1.0", markers = "python_version < \"3.8\""}
 packaging = ">=20.4"
+typing-extensions = "*"
 
 [package.extras]
 hiredis = ["hiredis (>=1.0.0)"]
@@ -1568,7 +1608,7 @@ python-versions = "*"
 
 [[package]]
 name = "sphinx"
-version = "4.4.0"
+version = "4.5.0"
 description = "Python documentation generator"
 category = "dev"
 optional = false
@@ -1702,7 +1742,7 @@ werkzeug = ">=0.11.15"
 
 [[package]]
 name = "tensorboardx"
-version = "2.4.1"
+version = "2.5"
 description = "TensorBoardX lets you watch Tensors Flow without Tensorflow"
 category = "main"
 optional = false
@@ -1711,6 +1751,7 @@ python-versions = "*"
 [package.dependencies]
 numpy = "*"
 protobuf = ">=3.8.0"
+six = "*"
 
 [[package]]
 name = "tensorflow"
@@ -1754,6 +1795,14 @@ category = "main"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "terminaltables"
+version = "3.1.10"
+description = "Generate simple tables in terminals from a nested list of strings."
+category = "main"
+optional = false
+python-versions = ">=2.6"
+
 [[package]]
 name = "texttable"
 version = "1.6.4"
@@ -1802,7 +1851,7 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "tqdm"
-version = "4.62.3"
+version = "4.63.1"
 description = "Fast, Extensible Progress Meter"
 category = "main"
 optional = false
@@ -1840,7 +1889,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "typing-extensions"
-version = "4.0.1"
+version = "4.1.1"
 description = "Backported and Experimental Type Hints for Python 3.6+"
 category = "main"
 optional = false
@@ -1848,31 +1897,31 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "urllib3"
-version = "1.26.8"
+version = "1.26.9"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
 
 [package.extras]
-brotli = ["brotlipy (>=0.6.0)"]
+brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"]
 secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"]
 socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "werkzeug"
-version = "2.0.3"
+version = "2.1.0"
 description = "The comprehensive WSGI web application library."
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.extras]
 watchdog = ["watchdog"]
 
 [[package]]
 name = "wrapt"
-version = "1.13.3"
+version = "1.14.0"
 description = "Module for decorators, wrappers and monkey patching."
 category = "main"
 optional = false
@@ -1897,6 +1946,14 @@ pandas = ["pandas"]
 plotting = ["graphviz", "matplotlib"]
 scikit-learn = ["scikit-learn"]
 
+[[package]]
+name = "xmltodict"
+version = "0.13.0"
+description = "Makes working with XML feel like you are working with JSON"
+category = "main"
+optional = false
+python-versions = ">=3.4"
+
 [[package]]
 name = "yarl"
 version = "1.7.2"
@@ -1933,7 +1990,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
 [metadata]
 lock-version = "1.1"
 python-versions = ">=3.7.1,<3.11"
-content-hash = "9243e6acc7477341296d163934bc99e0af5fae3f12adda96c5daa057a1cd33a5"
+content-hash = "002101f6087ef03167c900419fe42edafdc0d4c0e43fc392ecfdc7ea852e29b8"
 
 [metadata.files]
 absl-py = [
@@ -2031,16 +2088,16 @@ alabaster = [
     {file = "alabaster-0.7.12.tar.gz", hash = "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"},
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+    {file = "wrapt-1.14.0-cp39-cp39-win_amd64.whl", hash = "sha256:bb36fbb48b22985d13a6b496ea5fb9bb2a076fea943831643836c9f6febbcfdc"},
+    {file = "wrapt-1.14.0.tar.gz", hash = "sha256:8323a43bd9c91f62bb7d4be74cc9ff10090e7ef820e27bfe8815c57e68261311"},
 ]
 xgboost = [
     {file = "xgboost-1.4.2-py3-none-macosx_10_14_x86_64.macosx_10_15_x86_64.macosx_11_0_x86_64.whl", hash = "sha256:e8f1a366a403784afd30a56eb99a429cefc45d906943cd362025ccf942208e13"},
@@ -3540,6 +3592,10 @@ xgboost = [
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     {file = "xgboost-1.4.2.tar.gz", hash = "sha256:5a364c152095824445ac56a83fb7f7e75913b4bb128c2fcd99b85877c9f4f8fe"},
 ]
+xmltodict = [
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+]
 yarl = [
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diff --git a/pyproject.toml b/pyproject.toml
index 3a7168df..7db1053e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "aliby"
-version = "0.1.22"
+version = "0.1.25"
 description = "Process and analyse live-cell imaging data"
 authors = ["Alan Munoz <alan.munoz@ed.ac.uk>"]
 packages = [
@@ -25,9 +25,11 @@ h5py = "2.10"
 imageio = "2.8.0"
 omero-py = ">=5.6.2"
 zeroc-ice = "3.6.5"
-aliby-agora = "^0.2.22"
+aliby-agora = "^0.2.23"
 aliby-baby = "^0.1.7"
-aliby-post = "^0.1.21"
+aliby-post = "^0.1.25"
+p-tqdm = "^1.3.3"
+xmltodict = "^0.13.0"
 
 
 [tool.poetry.dev-dependencies]
-- 
GitLab