From d397a9668be029192616f5dcd04962b4a3f43048 Mon Sep 17 00:00:00 2001
From: Vonka <jakub.vonka@psi.ch>
Date: Wed, 3 Sep 2025 18:17:39 +0200
Subject: [PATCH] changes before migration

---
 .gitignore                         |  1 +
 src/cristallina/p22478/__init__.py | 37 +++++++++++++++++++++++++++++-
 src/cristallina/uscan.py           | 21 +++++++++++++----
 src/cristallina/utils.py           |  4 ++--
 4 files changed, 55 insertions(+), 8 deletions(-)

diff --git a/.gitignore b/.gitignore
index da9e8cc..bb67c65 100644
--- a/.gitignore
+++ b/.gitignore
@@ -37,6 +37,7 @@ htmlcov/*
 junit*.xml
 coverage.xml
 .pytest_cache/
+tests/cache_test/
 
 # Build and docs folder/files
 build/*
diff --git a/src/cristallina/p22478/__init__.py b/src/cristallina/p22478/__init__.py
index 2d1245b..c4fe73a 100644
--- a/src/cristallina/p22478/__init__.py
+++ b/src/cristallina/p22478/__init__.py
@@ -1 +1,36 @@
-print("p22478 module imported.")
\ No newline at end of file
+import os
+import json
+from pathlib import Path
+from collections import defaultdict, deque
+from copy import copy
+import time
+
+import scipy
+import numpy as np
+import pandas as pd
+from tqdm.notebook import tqdm
+import re
+
+from pathlib import Path
+
+import warnings
+
+from matplotlib import pyplot as plt
+import matplotlib as mpl
+
+import cristallina.utils as cu
+import cristallina as cr
+
+from loguru import logger
+
+from cristallina.uscan import UnfinishedScan
+
+from joblib import Parallel, delayed, Memory
+import sfdata
+from sfdata import SFProcFile, SFDataFile, SFDataFiles, SFScanInfo
+
+memory = Memory(location="/sf/cristallina/data/p22478/work/joblib", compress=2, verbose=2)
+pgroup = "p22478"
+
+print(f"p22478 module imported.")
+
diff --git a/src/cristallina/uscan.py b/src/cristallina/uscan.py
index 9c6c1d4..d4c0fe5 100644
--- a/src/cristallina/uscan.py
+++ b/src/cristallina/uscan.py
@@ -22,15 +22,26 @@ class UnfinishedScan(SFScanInfo):
             parser = JSONParser()
 
         self.info = info = parser.parse(content)
+        
 
         self.files = info["scan_files"]
-        self.parameters = info["scan_parameters"]
+        
+        try:
+            self.parameters = info["scan_parameters"]
+        except KeyError:
+            self.parameters = None
 
-        values = info["scan_values"]
-        values = [v for v in values if v]
+        try:
+            values = info["scan_values"]
+            values = [v for v in values if v]
+        except KeyError:
+            values = None
 
-        readbacks = info["scan_readbacks"]
-        readbacks = [r for r in readbacks if r]
+        try:
+            readbacks = info["scan_readbacks"]
+            readbacks = [r for r in readbacks if r]
+        except KeyError:
+            readbacks = None
 
         self.values = sfdata.utils.adjust_shape(values)
         self.readbacks = sfdata.utils.adjust_shape(readbacks)
diff --git a/src/cristallina/utils.py b/src/cristallina/utils.py
index 86c2059..c7fd491 100644
--- a/src/cristallina/utils.py
+++ b/src/cristallina/utils.py
@@ -454,7 +454,7 @@ class ROI:
     def height(self):
         return self.top - self.bottom
     
-    def shift(self, x: float, y: float, inplace=False):
+    def shift(self, x: float = 0, y: float = 0, inplace=False):
         """ Returns a new ROI that is shifted 
             by x to the left and by y pixels up.
             
@@ -473,7 +473,7 @@ class ROI:
             self.top = self.top + y
 
 
-    def expand(self, x: float, y: float, inplace=False):
+    def expand(self, x: float = 0, y: float = 0, inplace=False):
         """ Returns a new ROI that is expanded in x 
             to the left and right, and in y to the 
             top and bottom.